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Lai SK, Luo AC, Chiu IH, Chuang HW, Chou TH, Hung TK, Hsu JS, Chen CY, Yang WS, Yang YC, Chen PL. A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis. Comput Struct Biotechnol J 2024; 23:1562-1571. [PMID: 38650588 PMCID: PMC11035020 DOI: 10.1016/j.csbj.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4 and -DRB5) from 44 high-quality HPRC personal genome assemblies. For sequencing, we crafted HLA-specific probes and conducted capture-based targeted sequencing of the genomic DNA of the HPRC cohort, ensuring focused and comprehensive coverage of the HLA region of interest. We used publicly available short-read whole-genome sequencing (WGS) data from identical samples to offer a comparative perspective. To decipher the vast amount of sequencing data, we employed seven distinct software tools: OptiType, HLA-VBseq, HISAT genotype, SpecHLA, T1K, QzType, and DRAGEN. Each tool offers unique capabilities and algorithms for HLA genotyping, allowing comprehensive analysis and validation of the results. We then compared these results with benchmarks derived from personal genome assemblies. Our findings present a comprehensive four-field-resolution HLA allele annotation for 44 HPRC samples. Significantly, our innovative targeted next-generation sequencing (NGS) approach for HLA genes showed superior accuracy compared with conventional short-read WGS. An integrated analysis involving QzType, T1K, and DRAGEN was developed, achieving 100% accuracy for all 11 HLA genes. In conclusion, our study highlighted the combination of targeted short-read sequencing and astute computational analysis as a robust approach for HLA genotyping. Furthermore, the HPRC cohort has emerged as a valuable assembly-based reference in this realm.
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Affiliation(s)
- Sheng-Kai Lai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Allen Chilun Luo
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Hsuan Chiu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Wen Chuang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ting-Hsuan Chou
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsung-Kai Hung
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Chen
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ya-Chien Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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De’Ath A, Rees MT, Pritchard D. The history and evolution of HLA typing external proficiency testing schemes in UK NEQAS for H&I. Front Genet 2023; 14:1272618. [PMID: 37790700 PMCID: PMC10544324 DOI: 10.3389/fgene.2023.1272618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/29/2023] [Indexed: 10/05/2023] Open
Abstract
The UK National External Quality Assessment Service (NEQAS) provide an external proficiency testing (EPT) service for clinical laboratories. UK NEQAS for Histocompatibility and Immunogenetics (H&I) has been providing EPT schemes for over 45 years and has grown during this time to provide 19 EPT schemes. Accurate human leucocyte antigen (HLA) typing is critical to support safe clinical services, including transplantation, therefore high quality, relevant EPT schemes are required as part of a laboratory's quality assurance. This article reviews the development of the HLA typing EPT schemes, from the first HLA phenotyping scheme in 1975, via the first HLA genotyping scheme in 1992, through to the introduction in 2017 of HLA third field assessment results from next-generation sequencing technology. In addition, the introduction of EPT schemes to cover HLA associated diseases and pharmacogenetic reactions, including HLA-B27, HLA*B*57:01 and HLA-DQ for coeliac disease are discussed. The accuracy of laboratory EPT results for HLA phenotyping are >96% (2018-2022), HLA genotyping >99% (2020-2022), HLA-B27 testing >99% (2018-2022) and B*57:01 testing >99% (2017-2022). However, for HLA genotyping for coeliac disease 22%-46% of laboratories made errors in 2020-2022. On investigation, the high rate of unsatisfactory performance was attributed to laboratories lacking specific knowledge to interpret HLA genotyping results and accurately report HLA types for coeliac disease. A misleading commercial kit insert was also identified. The assessment of scheme results has uncovered several issues which have been addressed with the intention of educating participants and improving clinical services. The UK NEQAS for H&I EPT schemes have evolved over the past four decades to reflect changes in HLA typing technology, laboratory clinical practice and to cover post-analytical interpretative elements of HLA typing.
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Affiliation(s)
- A. De’Ath
- UK National External Quality Assessment Service for Histocompatibility and Immunogenetics, Welsh Blood Service, Cardiff, United Kingdom
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Martín Monreal MT, Hansen BE, Iversen PF, Enevold C, Ødum N, Sellebjerg F, Højrup P, Rode von Essen M, Nielsen CH. Citrullination of myelin basic protein induces a Th17-cell response in healthy individuals and enhances the presentation of MBP85-99 in patients with multiple sclerosis. J Autoimmun 2023; 139:103092. [PMID: 37506490 DOI: 10.1016/j.jaut.2023.103092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The post-translational modification citrullination has been proposed to play a role in the pathogenesis of multiple sclerosis (MS). Myelin basic protein (MBP) is a candidate autoantigen which is citrullinated to a minor extent under physiological conditions and hypercitrullinated in MS. We examined immune cell responses elicited by hypercitrullinated MBP (citMBP) in cultures of mononuclear cells from 18 patients with MS and 42 healthy donors (HDs). The immunodominant peptide of MBP, MBP85-99, containing citrulline in position 99, outcompeted the binding of native MBP85-99 to HLA-DR15, which is strongly linked to MS. Moreover, using the monoclonal antibody MK16 as probe, we observed that B cells and monocytes from HLA-DR15+ patients with MS presented MBP85-99 more efficiently after challenge with citMBP than with native MBP. Both citMBP and native MBP induced proliferation of CD4+ T cells from patients with MS as well as TNF-α production by their B cells and CD4+ T cells, and citrullination of MBP tended to enhance TNF-α secretion by CD4+ T cells from HLA-DR15+ patients. Unlike native MBP, citMBP induced differentiation into Th17 cells in cultures from HDs, while neither form of MBP induced Th17-cell differentiation in cultures from patients with MS. These data suggest a role for citrullination in the breach of tolerance to MBP in healthy individuals and in maintenance of the autoimmune response to MBP in patients with MS.
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Affiliation(s)
- María Teresa Martín Monreal
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Pernille F Iversen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christian Enevold
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Ødum
- LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Finn Sellebjerg
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Marina Rode von Essen
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
| | - Claus H Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section for Periodontology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Schor D, Porto LC, Roma EH, Castro-Alves J, Villela AP, Araújo AQC, Glória Bonecini-Almeida M. Putative role of HLA polymorphism among a Brazilian HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) population. Sci Rep 2023; 13:7659. [PMID: 37169817 PMCID: PMC10173239 DOI: 10.1038/s41598-023-34757-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/06/2023] [Indexed: 05/13/2023] Open
Abstract
Around ten million people are infected with HTLV-1 worldwide, and 1-4% develop HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), characterized by an important degeneration of the spinal cord, which can lead to death. Distinct HLA alleles have been associated with either HAM/TSP susceptibility or protection. However, these HLA alleles set may change according to the population studied. Brazil is the second country in the number of HTLV-1-infected people and there are few reports addressing the HLA influence on HTLV-1 infection as well as on disease outcome. The objective of this study was to evaluate the influence of HLA alleles as a risk factor for HAM/TSP and the proviral load (PVL) levels, clinical progression, and death outcomes in an admixed Brazilian population. The HLA-A, -B, -C, and -DRB1 were genotyped in 375 unrelated HTLV-1-infected individuals divided into asymptomatic carriers (AC) (n = 165) and HAM/TSP (n = 210) in a longitudinal cohort from 8 to 22 years of follow-up. Because locus B deviated from Hardy-Weinberg Equilibrium for the study groups, the results represented for HLA-B alleles were inconclusive. The alleles HLA-A*68 and -C*07 were related to HAM/TSP risk in multivariate analysis. The alleles HLA-A*33, and -A*36 were associated with protection against disease progression in HAM/TSP patients, while -C*12, -C*14, and -DRB1*08 were associated with increased risk of death. In the AC group, the presence of, -C*06 and -DRB1*15 alleles influenced an increased PVL, in an adjusted linear regression model, while -A*30, -A*34, -C*06, -C*17 and -DRB1*09 alleles were associated with increased PVL in HAM/TSP group compared to HAM/TSP individuals not carrying these alleles. All these alleles were also related to increased PVL associated with clinical progression outcome. Increased PVL associated with the death outcome was linked to the presence of HLA-A*30. PVL has been associated with HLA, and several alleles were related in AC and HAM/TSP patients with or without interacting with clinical progression outcomes. Understanding the prognostic value of HLA in HAM/TSP pathogenesis can provide important biomarkers tools to improve clinical management and contribute to the discovery of new therapeutic interventions.
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Affiliation(s)
- Doris Schor
- Laboratório de Imunologia e Imunogenética em Doenças Infecciosas, Instituto Nacional de Infectologia Evandro Chagas-INI/FIOCRUZ, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Luís Cristóvão Porto
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20950-000, Brazil
| | - Eric Henrique Roma
- Laboratório de Imunologia e Imunogenética em Doenças Infecciosas, Instituto Nacional de Infectologia Evandro Chagas-INI/FIOCRUZ, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Julio Castro-Alves
- Plataforma de Pesquisa Clínica, Instituto Nacional de Infectologia Evandro Chagas-INI/FIOCRUZ, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Anna Paula Villela
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20950-000, Brazil
| | - Abelardo Q C Araújo
- Laboratório de Pesquisa Clínica em Neuroinfecções, Instituto Nacional de Infectologia Evandro Chagas-INI/FIOCRUZ, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Maria Glória Bonecini-Almeida
- Laboratório de Imunologia e Imunogenética em Doenças Infecciosas, Instituto Nacional de Infectologia Evandro Chagas-INI/FIOCRUZ, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
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Raza A, Diehl SA, Krementsov DN, Case LK, Li D, Kost J, Ball RL, Chesler EJ, Philip VM, Huang R, Chen Y, Ma R, Tyler AL, Mahoney JM, Blankenhorn EP, Teuscher C. A genetic locus complements resistance to Bordetella pertussis-induced histamine sensitization. Commun Biol 2023; 6:244. [PMID: 36879097 PMCID: PMC9988836 DOI: 10.1038/s42003-023-04603-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Histamine plays pivotal role in normal physiology and dysregulated production of histamine or signaling through histamine receptors (HRH) can promote pathology. Previously, we showed that Bordetella pertussis or pertussis toxin can induce histamine sensitization in laboratory inbred mice and is genetically controlled by Hrh1/HRH1. HRH1 allotypes differ at three amino acid residues with P263-V313-L331 and L263-M313-S331, imparting sensitization and resistance respectively. Unexpectedly, we found several wild-derived inbred strains that carry the resistant HRH1 allotype (L263-M313-S331) but exhibit histamine sensitization. This suggests the existence of a locus modifying pertussis-dependent histamine sensitization. Congenic mapping identified the location of this modifier locus on mouse chromosome 6 within a functional linkage disequilibrium domain encoding multiple loci controlling sensitization to histamine. We utilized interval-specific single-nucleotide polymorphism (SNP) based association testing across laboratory and wild-derived inbred mouse strains and functional prioritization analyses to identify candidate genes for this modifier locus. Atg7, Plxnd1, Tmcc1, Mkrn2, Il17re, Pparg, Lhfpl4, Vgll4, Rho and Syn2 are candidate genes within this modifier locus, which we named Bphse, enhancer of Bordetella pertussis induced histamine sensitization. Taken together, these results identify, using the evolutionarily significant diversity of wild-derived inbred mice, additional genetic mechanisms controlling histamine sensitization.
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Affiliation(s)
- Abbas Raza
- Department of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Sean A Diehl
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA
| | - Dimitry N Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Laure K Case
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Dawei Li
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Jason Kost
- Catalytic Data Science, Charleston, SC, 29403, USA
| | - Robyn L Ball
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Rui Huang
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Chen
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Runlin Ma
- School of Life Sciences, University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Anna L Tyler
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - J Matthew Mahoney
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19129, USA
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Burlington, VT, 05405, USA.
- Pathology and Laboratory Medicine, University of Vermont, Burlington, VT, 05405, USA.
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Musa N, Govindasamy GS, Hoong CB, Annuar AA, Mohamed Noor DA, Daud NAA. A simple PCR-SSP method for detection of HLA-B*15:02, *15:13, and *15:21. TURKISH JOURNAL OF BIOCHEMISTRY 2023. [DOI: 10.1515/tjb-2022-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
Objectives
This study aims to develop a simple polymerase chain reaction (PCR) sequence-specific primer method, which will be used to genotype HLA-B*15:02, HLA-B*15:13, and HLA-B*15:21.
Methods
DNA was extracted from whole blood using a commercial DNA extraction kit. New specific primers were designed. The PCR was optimized for reproducibility and specificity. Parameters investigated included concentrations of MgCl2, primers concentration, and annealing temperature, to produce specific bands of interest. Known DNA samples were selected at random and tested using the PCR method.
Results
Simultaneously six duplex PCRs were successfully optimized using 1.0 mM MgCl2 and an annealing temperature of 62 °C. The method was also reproducible and specific. The results from the method showed 100% concordance with known DNA samples.
Conclusions
This study has successfully developed a simple and specific method to simultaneously genotype HLA-B*15:02, HLA-B*15:13, and HLA-B*15:21 using in-house developed PCR-SSP.
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Affiliation(s)
- Nurfadhlina Musa
- Human Genome Centre, School of Medical Sciences , Universiti Sains Malaysia , 16150 Kubang Kerian, Kota Bharu , Kelantan , Malaysia
| | - G Saravana Govindasamy
- Department of Pharmacy , Hospital Segamat , Ministry of Health Malaysia, Segamat , Johor , Malaysia
| | - Chew Beng Hoong
- Department of Pharmacy , Hospital Sultanah Bahiyah , Ministry of Health Malaysia, Alor Setar , Kedah , Malaysia
| | - Aziati Azwari Annuar
- Human Genome Centre, School of Medical Sciences , Universiti Sains Malaysia , 16150 Kubang Kerian, Kota Bharu , Kelantan , Malaysia
| | - Dzul Azri Mohamed Noor
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences , Universiti Sains Malaysia , 11800 USM , Pulau Pinang , Malaysia
| | - Nur Aizati Athirah Daud
- Human Genome Centre, School of Medical Sciences , Universiti Sains Malaysia , 16150 Kubang Kerian, Kota Bharu , Kelantan , Malaysia
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences , Universiti Sains Malaysia , 11800 USM , Pulau Pinang , Malaysia
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Cornaby C, Weimer ET. HLA Typing by Next-Generation Sequencing: Lessons Learned and Future Applications. Clin Lab Med 2022; 42:603-612. [PMID: 36368785 DOI: 10.1016/j.cll.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Caleb Cornaby
- McLendon Clinical Laboratories, UNC Hospitals, 101 Manning Drive, Chapel Hill, NC 27514, USA
| | - Eric T Weimer
- McLendon Clinical Laboratories, UNC Hospitals, 101 Manning Drive, Chapel Hill, NC 27514, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27514, USA.
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Increased Prevalence of Unstable HLA-C Variants in HIV-1 Rapid-Progressor Patients. Int J Mol Sci 2022; 23:ijms232314852. [PMID: 36499177 PMCID: PMC9741376 DOI: 10.3390/ijms232314852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
HIV-1 infection in the absence of treatment results in progression toward AIDS. Host genetic factors play a role in HIV-1 pathogenesis, but complete knowledge is not yet available. Since less-expressed HLA-C variants are associated with poor HIV-1 control and unstable HLA-C variants are associated with higher HIV-1 infectivity, we investigated whether there was a correlation between the different stages of HIV-1 progression and the presence of specific HLA-C allotypes. HLA-C genotyping was performed using allele-specific PCR by analyzing a treatment-naïve cohort of 96 HIV-1-infected patients from multicentric cohorts in the USA, Canada, and Brazil. HIV-1-positive subjects were classified according to their different disease progression status as progressors (Ps, n = 48), long-term non-progressors (LTNPs, n = 37), and elite controllers (ECs, n = 11). HLA-C variants were classified as stable or unstable according to their binding stability to β2-microglobulin/peptide complex. Our results showed a significant correlation between rapid progression to AIDS and the presence of two or one unstable HLA-C variants (p-value: 0.0078, p-value: 0.0143, respectively). These findings strongly suggest a link between unstable HLA-C variants both at genotype and at allele levels and rapid progression to AIDS. This work provides further insights into the impact of host genetic factors on AIDS progression.
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Saba N, Raja GK, Yusuf O, Rehman S, Munir S, Sajjad S, Mansoor A. Study of HLA class II loci reveals DQB1*03:03:02 as a risk factor for asthma in a Pakistani population. Int J Immunogenet 2022; 49:372-378. [PMID: 36271816 DOI: 10.1111/iji.12602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/12/2022] [Accepted: 10/09/2022] [Indexed: 11/29/2022]
Abstract
Asthma, a chronic inflammatory disorder of the lungs and airways, typically results from a combination of multiple environmental and genetic factors. Human leucocyte antigen (HLA) region on chromosome 6p21 encodes the most highly polymorphic loci in the human genome, encoding genes with central roles in the immune function where HLA loci are strongly associated with various immune-mediated diseases such as autoimmunity, allergies and infection. The alleles of HLA class II genes such as DRB1 and DQB1 are the key genetic markers in the development of asthma and have been extensively studied in different ethnicities of the world population. However, the genetic screening of HLA class II alleles and haplotypes in Pakistani asthmatics has not been studied so far. The aim of the present study was to screen the HLA class II DRB1 and DQB1 alleles in asthma cases and controls in a Pakistani population. Seven hundred and two healthy controls and asthma patients were genotyped for HLA class II by sequence-specific polymerase chain reaction assays. The HLA-DRB1 and HLA-DQB1 allele and haplotype frequencies were calculated, and their risk or protective association with asthma was determined. Two-locus haplotypes of DRB1 and DQB1 alleles were imputed using Arlequin version 3.1 software. The signals of association with asthma were stronger at the DQB1 locus as compared to DRB1. HLA DQB1*03:03:02 (odds ratio [OR] = 2.42, 95% confidence interval [CI] = 1.34-4.25) was significantly associated with an increased risk of asthma, as was the haplotype comprised allele DRB1*07:01-DQB1*03:03:02 (OR = 2.40, 95% CI = 1.25-4.62). In contrast, DQB1*06 (OR = 0.39, 95% CI = 0.22-0.70) and DQB1*06:02 (OR = 0.27, 95% CI = 0.10-0.71) emerged as protective alleles for asthma. Our data concludes that the HLA DQB1*03:03:02 allele was a risk allele for asthma, whereas two DQB1 alleles, DQB1*06 and DQB1*06:02, were associated with asthma protection. Our findings highlight a prominent role for HLA-DQB1 alleles in asthma pathogenesis in studied Pakistani cases. More studies, especially with a larger study cohort are needed to confirm the utility of HLA DQB1*03:03:02 as a predictive marker.
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Affiliation(s)
- Nusrat Saba
- Institute of Biomedical and Genetic Engineering (IBGE), G-9/1 24-Mauve Area Islamabad, Islamabad, Pakistan.,University Institute of Biochemistry and Biotechnology, Pir Mehar Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - Ghazala Kaukab Raja
- University Institute of Biochemistry and Biotechnology, Pir Mehar Ali Shah Arid Agriculture University Rawalpindi, Pakistan
| | - Osman Yusuf
- The Allergy and Asthma Institute of Pakistan, Islamabad, Pakistan
| | - Sadia Rehman
- Institute of Biomedical and Genetic Engineering (IBGE), G-9/1 24-Mauve Area Islamabad, Islamabad, Pakistan
| | - Saeeda Munir
- Institute of Biomedical and Genetic Engineering (IBGE), G-9/1 24-Mauve Area Islamabad, Islamabad, Pakistan
| | - Sumaira Sajjad
- Institute of Biomedical and Genetic Engineering (IBGE), G-9/1 24-Mauve Area Islamabad, Islamabad, Pakistan
| | - Atika Mansoor
- Institute of Biomedical and Genetic Engineering (IBGE), G-9/1 24-Mauve Area Islamabad, Islamabad, Pakistan
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Williams CL, Fareed R, Mortimer GLM, Aitken RJ, Wilson IV, George G, Gillespie KM, Williams AJK, Long AE. The longitudinal loss of islet autoantibody responses from diagnosis of type 1 diabetes occurs progressively over follow-up and is determined by low autoantibody titres, early-onset, and genetic variants. Clin Exp Immunol 2022; 210:151-162. [PMID: 36181724 PMCID: PMC9750828 DOI: 10.1093/cei/uxac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/03/2022] [Accepted: 09/30/2022] [Indexed: 01/12/2023] Open
Abstract
The clinical usefulness of post-diagnosis islet autoantibody levels is unclear and factors that drive autoantibody persistence are poorly defined in type 1 diabetes (T1D). Our aim was to characterise the longitudinal loss of islet autoantibody responses after diagnosis in a large, prospectively sampled UK cohort. Participants with T1D [n = 577] providing a diagnosis sample [range -1.0 to 2.0 years] and at least one post-diagnosis sample (<32.0 years) were tested for autoantibodies to glutamate decarboxylase 65 (GADA), islet antigen-2 (IA-2A), and zinc transporter 8 (ZnT8A). Select HLA and non-HLA SNPs were considered. Non-genetic and genetic factors were assessed by multivariable logistic regression models for autoantibody positivity at initial sampling and autoantibody loss at final sampling. For GADA, IA-2A, and ZnT8A, 70.8%, 76.8%, and 40.1%, respectively, remained positive at the final sampling. Non-genetic predictors of autoantibody loss were low baseline autoantibody titres (P < 0.0001), longer diabetes duration (P < 0.0001), and age-at-onset under 8 years (P < 0.01--0.05). Adjusting for non-genetic covariates, GADA loss was associated with low-risk HLA class II genotypes (P = 0.005), and SNPs associated with autoimmunity RELA/11q13 (P = 0.017), LPP/3q28 (P = 0.004), and negatively with IFIH1/2q24 (P = 0.018). IA-2A loss was not associated with genetic factors independent of other covariates, while ZnT8A loss was associated with the presence of HLA A*24 (P = 0.019) and weakly negatively with RELA/11q13 (P = 0.049). The largest longitudinal study of islet autoantibody responses from diagnosis of T1D shows that autoantibody loss is heterogeneous and influenced by low titres at onset, longer duration, earlier age-at-onset, and genetic variants. These data may inform clinical trials where post-diagnosis participants are recruited.
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Affiliation(s)
- C L Williams
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - R Fareed
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - G L M Mortimer
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - R J Aitken
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - I V Wilson
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - G George
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - K M Gillespie
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - A J K Williams
- Diabetes and Metabolism, Translational Health Sciences, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK
| | - The BOX Study Group
BallavChitrabhanuDrBucks Healthcare Trust, UKDuttaAtanuDrBucks Healthcare Trust, UKRussell-TaylorMichelleDrBucks Healthcare Trust, UKBesserRachelDrOxford University Hospitals Trust UK, UKBursellJamesDrMilton Keynes University Hospital, UKChandranShanthiDrMilton Keynes University Hospital, UKPatelSejalDrWexham Park Hospital, UKSmithAnneDrNorthampton General Hospital, UKKenchaiahManoharaDrNorthampton General Hospital, UKMargabanthuGomathiDrKettering General Hospital, UKKavvouraFoteiniDrRoyal Berkshire Hospital, UKYaliwalChandanDrRoyal Berkshire Hospital, UK
| | - A E Long
- Correspondence: Dr Anna. E. Long. Diabetes and Metabolism, Bristol Medical School, University of Bristol, Level 2, Learning and Research Building, Southmead Hospital, Bristol BS10 5NB, UK.
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11
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Hu S, Shao Z, Ni W, Sun P, Qiao J, Wan H, Huang Y, Liu X, Zhai H, Xiao M, Sun B. The KIR2DL2/HLA-C1C1 Gene Pairing Is Associated With an Increased Risk of SARS-CoV-2 Infection. Front Immunol 2022; 13:919110. [PMID: 35874712 PMCID: PMC9301464 DOI: 10.3389/fimmu.2022.919110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 is the causative agent for the global COVID-19 pandemic; however, the interaction between virus and host is not well characterized. Natural killer cells play a key role in the early phase of the antiviral response, and their primary functions are dependent on signaling through the killer cell immunoglobulin-like receptor (KIR). This study measured the association between KIR/HLA class I ligand pairings and the occurrence and development of COVID-19. DNA of blood samples from 257 COVID-19 patients were extracted and used to detect KIR and HLA-C gene frequencies using single strain sequence-specific primer (SSP) PCR. The frequency of these genes was compared among 158 individuals with mild COVID-19, 99 with severe disease, and 98 healthy controls. The frequencies of KIR2DL2 (P=0.04, OR=1.707), KIR2DS3 (P=0.047, OR=1.679), HLA-C1C1 (P<0.001, OR=3.074) and the KIR2DL2/HLA-C1C1 pairing (P=0.038, OR=2.126) were significantly higher in the COVID-19 patients than the healthy controls. At the same time, the frequency of KIR2DL3+KIR2DL2-/HLA-C1+Others+ was lower in COVID-19 patients than in healthy individuals (P=0.004, OR=0.477). These results suggest that the protective effect of KIR2DL3 against SARS-CoV-2 infection is related to the absence of the KIR2DL2 gene. This study found no correlation between the frequencies of these genes and COVID-19 pathogenesis. Global statistical analysis revealed that the incidence of COVID-19 infection was higher in geographic regions with a high frequency of KIR2DL2. Together these results suggest that the KIR2DL2/HLA-C1C1 gene pairing may be a risk factor for SARS-CoV-2 infection.
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Affiliation(s)
- Song Hu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Zuoyu Shao
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hepatic Disease Institute, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, China
| | - Wei Ni
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hepatic Disease Institute, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, China
| | - Pan Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- Hepatic Disease Institute, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, China
| | - Jialu Qiao
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Hexing Wan
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Yi Huang
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Xiaolong Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Haoyang Zhai
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Mingzhong Xiao
- Hepatic Disease Institute, Hubei Key Laboratory of Theoretical and Applied Research of Liver and Kidney in Traditional Chinese Medicine, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China
- Hepatic Disease Institute, Hubei Province Academy of Traditional Chinese Medicine, Wuhan, China
- *Correspondence: Binlian Sun, ; Mingzhong Xiao,
| | - Binlian Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- *Correspondence: Binlian Sun, ; Mingzhong Xiao,
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12
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Louvanto K, Baral P, Burchell A, Ramanakumar A, El-Zein M, Tellier PP, Coutlée F, Roger M, Franco EL. Role of Human Leukocyte Antigen Allele Sharing in Human Papillomavirus Infection Transmission Among Heterosexual Couples: Findings From the Hitch Cohort Study. J Infect Dis 2022; 226:1175-1183. [PMID: 35363864 PMCID: PMC9518836 DOI: 10.1093/infdis/jiac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/29/2022] [Indexed: 11/12/2022] Open
Abstract
Background Human leukocyte antigen (HLA) polymorphism influences innate and adaptive immune responses. Among heterosexual couples in the HPV Infection and Transmission Among Couples Through Heterosexual Activity (HITCH) cohort study, we examined whether allele sharing in a couple predicted the partners’ infections with the same human papillomavirus (HPV) type. Methods We tested genital samples from 271 couples for 36 HPV genotypes by polymerase chain reaction. We used direct DNA sequencing to type HLA-B07, -DRB1, -DQB1 and -G. Generalized estimating equations were used to examine the associations between the extent of allele sharing and HPV type concordance in which at least 1 of the partners was HPV positive. Results We identified 106 different HLA alleles. The most common HLA alleles among couples were G*01:01:01 (95.6%), G*01:01:02 (60.1%), DQB1*03:01 (57.2%), and DRB1*07:01 (46.9%). Allele sharing was as follows: 19.6% shared none, 43.2% shared 1 only, 25.1% shared 2, and 12.5% shared 3–5. Irrespective of HLA class, grouped or in combination, the extent of allele sharing was not a significant predictor of type-specific HPV concordance in a couple (odds ratio, 1.1 [95% confidence interval, .5–2.1], for 3–5 vs none). Conclusions We found no evidence that the extent of HLA allele concordance influences the likelihood of HPV transmission in newly formed heterosexual couples.
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Affiliation(s)
- Karolina Louvanto
- Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada.,Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Technology, Tampere, Finland.,Department of Obstetrics and Gynaecology, Tampere University Hospital, Tampere, Finland
| | - Prativa Baral
- Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada
| | - Ann Burchell
- Ontario HIV Treatment Network, Toronto, Ontario, Canada
| | | | - Mariam El-Zein
- Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada
| | | | - Francois Coutlée
- Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada.,Centre de recherche du CHUM et Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Michel Roger
- Centre de recherche du CHUM et Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Eduardo L Franco
- Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada
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13
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Juliani MPB, Rocha AB, Zendrini GO, Bello VA, Poli-Frederico RC, Silva AVD. Evaluation of the genetic variant - 889 C > T Of Il-1α in migraine - partial analysis. HEADACHE MEDICINE 2022. [DOI: 10.48208/headachemed.2021.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
IntroductionThe pathophysiology of migraine integrates inflammatory and genetic aspects, with interleukin-1α being a component of this picture. This pro-inflammatory cytokine, responsible for inducing pyrogenic, hematological, and metabolic phenomena, is produced by macrophages and monocytes. Genetic variants, which can be found in the regulatory region of the gene for this substance, have clinical implications in different systems.ObjectiveTo evaluate the frequency of the -889C>T genetic variant of IL-1α and its association with clinical variables related to migraine. MethodsProspective case-control study composed of migraine patients and healthy controls aged between 18 and 60 years of age. Project approved by the Research Ethics Committee of PUCPR (No. 3,029,972). Demographic, clinical data on migraine classification and characteristics were collected using a structured form and validated questionnaires on anxiety (STAIY2), depression (BDI) and migraine-related disability (MIDAS). Genetic evaluation was performed with blood or saliva samples that were subjected to polymerase chain reaction (PCR), followed by electrophoresis in 1.5% agarose gel. Categorical data were analyzed by chi-square test or Fisher's exact test and continuous data by t-test or Mann-Whitney test. ResultsA total of 156 participants, 73 migraineurs and 83 controls, were evaluated. The -889C>T variant of IL-1α was not associated with increased susceptibility to migraine when evaluated in allelic, codominant, dominant, or recessive models. The C allele, the lowest producer of the cytokine, was associated with a higher frequency of osmophobia in patients with migraine (65.5% vs. 48.2%; p=0.038). ConclusionNo association was identified between the -889C>T variant of IL-1α and susceptibility to migraine. Its effect on osmophobia should be further investigated. However, the present work is a partial analysis whose main limitation is the small sample size.
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14
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Contribution of HLA class II genes, DRB4*01:01, DRB1*07:01, and DQB1*03:03:2 to clinical features of Vitiligo disease in Iranian population. Mol Biol Rep 2021; 49:171-178. [PMID: 34686989 DOI: 10.1007/s11033-021-06855-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/19/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Vitiligo is a multifactorial depigmentation condition, which is due to skin melanocyte destruction. Increased expression of HLA class II genes in patients with pre-lesions of Vitiligo suggests a crucial role for the participation of immune response in Vitiligo development. Recent studies progressively focused on HLA-DRB1 and DQB1 genes. In this study, we have evaluated the association and role of HLA-DRB4*01:01, -DRB1*07:01, and -DQB1*03:03:2 genes in different clinical subtypes of Vitiligo in the Iranian population. METHODS First, Genomic DNA from peripheral blood of 125 unrelated Vitiligo patients and 100 unrelated healthy controls were extracted through the salting-out method. Then, HLA class II genotyping was performed using the sequence-specific primer PCR method. Finally, the clinical relevance of the testing for these genotypes was evaluated by applying the PcPPV (prevalence-corrected positive predictive value) formula. RESULTS Our results indicated the positive associations of DRB4*01:01 and DRB1*07:01 allelic genes with early-onset Vitiligo (p = 0.024 and 0.022, respectively). DRB4*01:01 also showed strong protection against late-onset Vitiligo (p = 0.0016, RR = 0.360). Moreover, our data revealed that the DRB1*07:01 increases the susceptibility to Sporadic Vitiligo (p = 0.030, RR = 1.702). Furthermore, our findings proposed that elevated vulnerability of Vitiligo patients due to DRB4*01:01 and DRB1*07:01 alleles maybe is correlated with the presence of amino acid Arginine at position 71 at pocket 4 on the antigen-binding site of the HLA-DRB1 receptor. CONCLUSION Our findings on different subtypes of Vitiligo suggest that, despite a more apparent autoimmune involvement, a non-autoimmune nature for the etiology of Vitiligo should also be considered.
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15
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Cheng Y, Grueber C, Hogg CJ, Belov K. Improved high-throughput MHC typing for non-model species using long-read sequencing. Mol Ecol Resour 2021; 22:862-876. [PMID: 34551192 PMCID: PMC9293008 DOI: 10.1111/1755-0998.13511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/26/2021] [Accepted: 09/06/2021] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) plays a critical role in the vertebrate immune system. Accurate MHC typing is critical to understanding not only host fitness and disease susceptibility, but also the mechanisms underlying host‐pathogen co‐evolution. However, due to the high degree of gene duplication and diversification of MHC genes, it is often technically challenging to accurately characterise MHC genetic diversity in non‐model species. Here we conducted a systematic review to identify common issues associated with current widely used MHC typing approaches. Then to overcome these challenges, we developed a long‐read based MHC typing method along with a new analysis pipeline. Our approach enables the sequencing of fully phased MHC alleles spanning all key functional domains and the separation of highly similar alleles as well as the removal of technical artefacts such as PCR heteroduplexes and chimeras. Using this approach, we performed population‐scale MHC typing in the Tasmanian devil (Sarcophilus harrisii), revealing previously undiscovered MHC functional diversity in this endangered species. Our new method provides a better solution for addressing research questions that require high MHC typing accuracy. Since the method is not limited by species or the number of genes analysed, it will be applicable for studying not only the MHC but also other complex gene families.
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Affiliation(s)
- Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Catherine Grueber
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,San Diego Zoo Wildlife Alliance, San Diego, California, USA
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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16
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Cornaby C, Schmitz JL, Weimer ET. Next-generation sequencing and clinical histocompatibility testing. Hum Immunol 2021; 82:829-837. [PMID: 34521569 DOI: 10.1016/j.humimm.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
Histocompatibility testing is essential for donor identification and risk assessment in solid organ and hematopoietic stem cell transplant. Additionally, it is useful for identifying donor specific alleles for monitoring donor specific antibodies in post-transplant patients. Next-generation sequence (NGS) based human leukocyte antigen (HLA) typing has improved many aspects of histocompatibility testing in hematopoietic stem cell and solid organ transplant. HLA disease association testing and research has also benefited from the advent of NGS technologies. In this review we discuss the current impact and future applications of NGS typing on clinical histocompatibility testing for transplant and non-transplant purposes.
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Affiliation(s)
- Caleb Cornaby
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA
| | - John L Schmitz
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA; Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Eric T Weimer
- McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, USA; Department of Pathology & Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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17
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Association of HLA-B*51:01, HLA-B*55:01, CYP2C9*3, and Phenytoin-Induced Cutaneous Adverse Drug Reactions in the South Indian Tamil Population. J Pers Med 2021; 11:jpm11080737. [PMID: 34442381 PMCID: PMC8400937 DOI: 10.3390/jpm11080737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
Phenytoin (PHT) is one of the most commonly reported aromatic anti-epileptic drugs (AEDs) to cause cutaneous adverse reactions (CADRs), particularly severe cutaneous adverse reactions (SCARs). Although human leukocyte antigen (HLA)-B*15:02 is associated with PHT-induced Steven Johnson syndrome/toxic epidermal necrosis (SJS/TEN) in East Asians, the association is much weaker than it is reported for carbamazepine (CBZ). In this study, we investigated the association of pharmacogenetic variants of the HLA B gene and CYP2C9*3 with PHT-CADRs in South Indian epileptic patients. This prospective case-controlled study included 25 PHT-induced CADRs, 30 phenytoin-tolerant patients, and 463 (HLA-B) and 82 (CYP2C9*3) normal-controls from previous studies included for the case and normal-control comparison. Six SCARs cases and 19 mild-moderate reactions were observed among the 25 cases. Pooled data analysis was performed for the HLA B*51:01 and PHT-CADRs associations. The Fisher exact test and multivariate binary logistic regression analysis were used to identify the susceptible alleles associated with PHT-CADRs. Multivariate analysis showed that CYP2C9*3 was significantly associated with overall PHT-CADRs (OR = 12.00, 95% CI 2.759–84.87, p = 003). In subgroup analysis, CYP2C9*3 and HLA B*55:01 were found to be associated with PHT-SCARs (OR = 12.45, 95% CI 1.138–136.2, p = 0.003) and PHT-maculopapular exanthema (MPE) (OR = 4.041, 95% CI 1.125–15.67, p = 0.035), respectively. Pooled data analysis has confirmed the association between HLA B*51:01/PHT-SCARs (OR = 6.273, 95% CI 2.24–16.69, p = <0.001) and HLA B*51:01/PHT-overall CADRs (OR = 2.323, 95% CI 1.22–5.899, p = 0.037). In this study, neither the case nor the control groups had any patients with HLA B*15:02. The risk variables for PHT-SCARs, PHT-overall CADRs, and PHT-MPE were found to be HLA B*51:01, CYP2C9*3, and HLA B*55:01, respectively. These alleles were identified as the risk factors for the first time in the South Indian Tamil population for PHT-CADRs. Further investigation is warranted to establish the clinical relevance of these alleles in this population with larger sample size.
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18
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Chandra A, Das S, Mazumder S, Senapati S, Chatterjee G, Chatterjee R. Functional Mapping of Genetic Interactions between HLA-Cw6 and LCE3A in Psoriasis. J Invest Dermatol 2021; 141:2630-2638.e7. [PMID: 34029573 DOI: 10.1016/j.jid.2021.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/31/2022]
Abstract
Functional studies to delineate the molecular mechanisms of causal genetic variants are the main focus in the post-GWAS era. Previous GWASs have identified >50 susceptibility loci associated with psoriasis. Functional understanding of the biology underlying the disease risk of most of these associated loci is unclear. In this study, we identified a regulatory SNP at the putative enhancer of the LCE3A gene within the epidermal differentiation complex that showed epistatic interaction with HLA-Cw6. The variant allele disrupted signal transducer and activator of transcription 3 binding to the region, thereby regulating the expression of the downstream LCE3A gene. Electrophoretic mobility shift and pulldown assay confirmed the preferential binding of signal transducer and activator of transcription 3 to the DNA with a wild-type allele compared with the DNA with a variant allele. The reporter assay further validated the IL-6‒stimulated phosphorylated signal transducer and activator of transcription 3‒mediated LCE3A activation in the presence of the wild-type allele. Interestingly, the presence of the HLA-Cw6 allele leads to IL-6‒mediated phosphorylation of signal transducer and activator of transcription 3, followed by its nuclear localization in the epidermal keratinocytes of psoriatic skin, suggesting indirect interaction of the HLA-Cw6 allele and a regulatory SNP upstream of the LCE3A gene. This study reflects an interesting approach to dissecting the molecular mechanism underlying the genetic interaction observed between HLA-Cw6 and LCE3A in psoriasis pathogenesis.
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Affiliation(s)
- Aditi Chandra
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Shantanab Das
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Sayani Mazumder
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Swapan Senapati
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India
| | - Gobinda Chatterjee
- Department of Dermatology, Institute of Post Graduate Medical Education & Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Biological Sciences Division, Indian Statistical Institute, Kolkata, India.
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19
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Creary LE, Sacchi N, Mazzocco M, Morris GP, Montero-Martin G, Chong W, Brown CJ, Dinou A, Stavropoulos-Giokas C, Gorodezky C, Narayan S, Periathiruvadi S, Thomas R, De Santis D, Pepperall J, ElGhazali GE, Al Yafei Z, Askar M, Tyagi S, Kanga U, Marino SR, Planelles D, Chang CJ, Fernández-Viña MA. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report. Hum Immunol 2021; 82:505-522. [PMID: 34030896 DOI: 10.1016/j.humimm.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK; Faculty of Life Sciences and Medicine, King's College London, University of London, England, UK
| | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | | | - Clara Gorodezky
- Laboratory of Immunology and Immunogenetics, Fundación Comparte Vida, A.C. Mexico City, Mexico
| | | | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, USA
| | | | - Jennifer Pepperall
- Welsh Transplant and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, United Kingdom
| | - Gehad E ElGhazali
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical center, Dallas, USA
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Susana R Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain; Grupo Español de Trabajo en Histocompatibilidad e Inmunología del Trasplante (GETHIT), Spanish Society for Immunology, Madrid, Spain
| | | | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
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20
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Leal B, Carvalho C, Ferreira AM, Nogueira M, Brás S, Silva BM, Selores M, Costa PP, Torres T. Serum Levels of miR-146a in Patients with Psoriasis. Mol Diagn Ther 2021; 25:475-485. [PMID: 33937970 DOI: 10.1007/s40291-021-00531-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND Psoriasis is an immune-mediated disease with interactions between genetic and environmental factors. An increasing number of studies are demonstrating the importance of microRNAs (miRNAs) in the pathogenesis of psoriasis. miR-146a, a dominant negative regulator of inflammation, has been consistently reported as overexpressed in the skin and peripheral blood mononuclear cells (PBMCs) of patients with psoriasis. Expression and/or function of this miRNA is highly influenced by genetic variations, some of which have already been associated with susceptibility to psoriasis. OBJECTIVE We sought to study the importance of miR-146a in patients with moderate-to-severe psoriasis and to understand the impact of rs57095329 and rs2910164 polymorphisms in a psoriatic Portuguese population. METHODS miR-146a circulating levels were quantified using molecular biology techniques in 99 patients with moderate-to-severe psoriasis (35 female, 64 male; age 47.4 ± 10.9 years) and 78 healthy individuals (52 female, 26 male; age 42.4 ± 10.1 years). miRNA expression was correlated with clinicopathological features as well as with genetic data such as the presence of human leukocyte antigen (HLA)-C*0602 allele and two miR-146a polymorphisms (rs2910164 and rs57095329). RESULTS miR-146a serum levels were 3.7-fold higher in patients with psoriasis than in controls (p < 0.0001, area under the curve [AUC] 0.75; 95% confidence interval [CI] 0.66-0.83). Of note, miR-146a circulating levels positively correlated with Psoriasis Area and Severity Index (p < 0.05) and body surface area (p < 0.05) indexes. No variations in miR-146a levels were observed with rs2910164 and rs57095329 genotypes. CONCLUSION Circulating miR-146a levels were upregulated in patients with psoriasis, especially in those with active disease. To the best of our knowledge, this is the largest study with a homogenous psoriasis population, and our data could shed light on the pathogenesis of psoriasis, paving the way for new avenues for disease treatment.
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Affiliation(s)
- Bárbara Leal
- UMIB, Instituto de Ciências Biomédicas Abel Salazar [ICBAS], Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Lab. Imunogenética, DPIM, ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Cláudia Carvalho
- UMIB, Instituto de Ciências Biomédicas Abel Salazar [ICBAS], Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Lab. Imunogenética, DPIM, ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Ana Marta Ferreira
- UMIB, Instituto de Ciências Biomédicas Abel Salazar [ICBAS], Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Lab. Imunogenética, DPIM, ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Miguel Nogueira
- Dermatology Department, Centro Hospitalar Universitário do Porto, Largo Prof. Abel Salazar, 4099-003, Porto, Portugal
| | - Sandra Brás
- Lab. Imunogenética, DPIM, ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Berta M Silva
- UMIB, Instituto de Ciências Biomédicas Abel Salazar [ICBAS], Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Lab. Imunogenética, DPIM, ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Manuela Selores
- UMIB, Instituto de Ciências Biomédicas Abel Salazar [ICBAS], Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Dermatology Department, Centro Hospitalar Universitário do Porto, Largo Prof. Abel Salazar, 4099-003, Porto, Portugal
| | - Paulo P Costa
- UMIB, Instituto de Ciências Biomédicas Abel Salazar [ICBAS], Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Lab. Imunogenética, DPIM, ICBAS-UPorto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.,Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge-Porto, Rua Pedro Nunes, n.º 88, 4099-032, Porto, Portugal
| | - Tiago Torres
- UMIB, Instituto de Ciências Biomédicas Abel Salazar [ICBAS], Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal. .,Dermatology Department, Centro Hospitalar Universitário do Porto, Largo Prof. Abel Salazar, 4099-003, Porto, Portugal. .,Dermatology Research Unit, Centro Hospitalar Universitário do Porto, Largo Prof. Abel Salazar, 4099-003, Porto, Portugal.
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21
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Parry HM, Dowell AC, Zuo J, Verma K, Kinsella FAM, Begum J, Croft W, Sharma-Oates A, Pratt G, Moss P. PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity. PLoS Pathog 2021; 17:e1009349. [PMID: 33662046 PMCID: PMC7963093 DOI: 10.1371/journal.ppat.1009349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/16/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
PD-1 is expressed on exhausted T cells in cancer patients but its physiological role remains uncertain. We determined the phenotype, function and transcriptional correlates of PD-1 expression on cytomegalovirus-specific CD4+ T cells during latent infection. PD-1 expression ranged from 10-85% and remained stable over time within individual donors. This 'setpoint' was correlated with viral load at primary infection. PD-1+ CD4+ T cells display strong cytotoxic function but generate low levels of Th1 cytokines which is only partially reversed by PD-1 blockade. TCR clonotypes showed variable sharing between PD-1+ and PD-1- CMV-specific cells indicating that PD-1 status is defined either during T cell priming or subsequent clonal expansion. Physiological PD-1+ CD4+ T cells therefore display a unique 'high cytotoxicity-low cytokine' phenotype and may act to suppress viral reactivation whilst minimizing tissue inflammation. Improved understanding of the physiological role of PD-1 will help to delineate the mechanisms, and potential reversal, of PD-1+ CD4+ T cell exhaustion in patients with malignant disease.
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Affiliation(s)
- Helen M. Parry
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alexander C. Dowell
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jianmin Zuo
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kriti Verma
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Francesca A. M. Kinsella
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jusnara Begum
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Wayne Croft
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Computational Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Archana Sharma-Oates
- Centre for Computational Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Institute of Cancer & Genomics, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Guy Pratt
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Paul Moss
- Institute of Immunology & Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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22
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Pharmacogenetic and Association Studies on the Influence of HLA Alleles and Rivastigmine on the Iranian Patients with Late-Onset Alzheimer's Disease. Mol Neurobiol 2021; 58:2792-2802. [PMID: 33502736 DOI: 10.1007/s12035-021-02295-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder affecting cognitive function. A number of allelic genes from HLA complex have shown variable associations with AD in different populations. In this study, we investigated the association of DQB1*06:00/x, DRB1*04:00/x, DRB1*15:00/x, and B*07:00/x genotypes with AD and their relevance to the efficacy of rivastigmine treatment in the Iranian population. Our findings suggest that DQB1*06:00/x genotype offers strong protection against AD (P = 0.0074), while B*07:00/x genotype imposes a significant susceptibility for sporadic Alzheimer's disease (SAD) (P = 0.009). Interestingly, B*07:00/x genotype does not show any apparent associations with familial Alzheimer's disease (FAD). Our studies also suggest a pharmacogenetic relationship between drug treatment and presence of a particular genotype in the Iranian LOAD patient population. The Clinical Dementia Rating analysis showed that LOAD patients carrying DRB1*04:00/x genotype tend to display a downward trend in the disease severity and symptoms after 2-year follow-up with rivastigmine treatment. Moreover, in our total patient population, the carriers of DQB1*06:00/x and B*07:00/x alleles have better and worse responses to rivastigmine respectively. We also measured the clinical relevance of the testing for these genotypes employing prevalence-corrected positive predictive value (PcPPV) formula. The PcPPV of testing for DQB1*06:00/x in the Iranian LOAD patients was 1.17% which means that people carrying this genotype have half of the probability of the absolute risk for developing LOAD, whereas the PcPPV of testing for B*07:00/x was 4.45% for SAD, which can be interpreted as a doubling chance for developing LOAD among the Iranian population carrying this genotype. These results also suggest that DQβ1 peptide containing positively charged AAs histidine30 and arginine55 and HLA class I β chain containing negatively charges aspartic acid114 and glutamic acid45,152 in their binding groove plays important roles in protection against and susceptibility for LOAD respectively.
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23
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Kachooei-Mohaghegh-Yaghoobi L, Rezaei-Rad F, Sadeghniiat-Haghighi K, Zamani M. The impact of the HLA DQB1 gene and amino acids on the development of narcolepsy. Int J Neurosci 2020; 132:706-713. [PMID: 33045884 DOI: 10.1080/00207454.2020.1835903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Narcolepsy is a chronic neurological and a genetic disorder of autoimmune origin, which is characterized by five main symptoms, including excessive day time sleepiness, sudden loss of muscle tone or cataplexy, sleep paralysis, hypnagogic hallucinations, and disturbed nocturnal sleep. While there are several diagnostic tests for Narcolepsy such as MSLT (mean sleep latency test), polysomnography and low range of hypocretin in cerebrospinal fluid (CSF), sensitivity and specificity in these methodologies are not sufficient enough. Therefore, methods with higher sensitivity for the accurate diagnosis and confirmation of the disease are necessary. METHODS According to the infrequent prevalence of narcolepsy disease, we scheduled a case-control association study with 20 narcoleptic patients and 150 healthy individuals in a high-resolution HLA typing procedure employing SSP-PCR. RESULTS Our study demonstrates that the DQB1*06:02 allele provides the highest susceptibility with absolute risk of 0.13%, for Narcolepsy (P = 1x10-14, RR = 60.5, PcPPV = 0.13%), while, HLA-DQB1* 03:05 allele presents protection to Narcolepsy (P = 1x10-4, PcPPV = 3.19x10-4%). Furthermore, for the first time, the AA analysis displayed that AA serine182 and threonine185 located on epitope of DQβ1 chain receptor (DQB1Ser182,Thr185) present significant susceptibility for Narcolepsy (Pc= 87.03 × 10-13, PcPPV = 0.024%) while, asparagine182 located on epitope of DQβ1 protein receptor (DQB1Asn182) confers the highest protection against development of Narcolepsy (Pc= 2.16 × 10-5, PcPPV = 0.0012%). CONCLUSION Thus, this can be proposed that the polymorphic differences in the epitope of the HLA receptor could contribute to their differential association with the Narcolepsy in Iranian population.
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Affiliation(s)
| | - Fatemeh Rezaei-Rad
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mahdi Zamani
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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24
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Balcha SA, Demisse AG, Mishra R, Vartak T, Cousminer DL, Hodge KM, Voight BF, Lorenz K, Schwartz S, Jerram ST, Gamper A, Holmes A, Wilson HF, Williams AJK, Grant SFA, Leslie RD, Phillips DIW, Trimble ER. Type 1 diabetes in Africa: an immunogenetic study in the Amhara of North-West Ethiopia. Diabetologia 2020; 63:2158-2168. [PMID: 32705316 PMCID: PMC7476916 DOI: 10.1007/s00125-020-05229-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022]
Abstract
AIMS/HYPOTHESIS We aimed to characterise the immunogenic background of insulin-dependent diabetes in a resource-poor rural African community. The study was initiated because reports of low autoantibody prevalence and phenotypic differences from European-origin cases with type 1 diabetes have raised doubts as to the role of autoimmunity in this and similar populations. METHODS A study of consecutive, unselected cases of recently diagnosed, insulin-dependent diabetes (n = 236, ≤35 years) and control participants (n = 200) was carried out in the ethnic Amhara of rural North-West Ethiopia. We assessed their demographic and socioeconomic characteristics, and measured non-fasting C-peptide, diabetes-associated autoantibodies and HLA-DRB1 alleles. Leveraging genome-wide genotyping, we performed both a principal component analysis and, given the relatively modest sample size, a provisional genome-wide association study. Type 1 diabetes genetic risk scores were calculated to compare their genetic background with known European type 1 diabetes determinants. RESULTS Patients presented with stunted growth and low BMI, and were insulin sensitive; only 15.3% had diabetes onset at ≤15 years. C-peptide levels were low but not absent. With clinical diabetes onset at ≤15, 16-25 and 26-35 years, 86.1%, 59.7% and 50.0% were autoantibody positive, respectively. Most had autoantibodies to GAD (GADA) as a single antibody; the prevalence of positivity for autoantibodies to IA-2 (IA-2A) and ZnT8 (ZnT8A) was low in all age groups. Principal component analysis showed that the Amhara genomes were distinct from modern European and other African genomes. HLA-DRB1*03:01 (p = 0.0014) and HLA-DRB1*04 (p = 0.0001) were positively associated with this form of diabetes, while HLA-DRB1*15 was protective (p < 0.0001). The mean type 1 diabetes genetic risk score (derived from European data) was higher in patients than control participants (p = 1.60 × 10-7). Interestingly, despite the modest sample size, autoantibody-positive patients revealed evidence of association with SNPs in the well-characterised MHC region, already known to explain half of type 1 diabetes heritability in Europeans. CONCLUSIONS/INTERPRETATION The majority of patients with insulin-dependent diabetes in rural North-West Ethiopia have the immunogenetic characteristics of autoimmune type 1 diabetes. Phenotypic differences between type 1 diabetes in rural North-West Ethiopia and the industrialised world remain unexplained.
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Affiliation(s)
- Shitaye A Balcha
- Department of Internal Medicine, Gondar University Hospital, Gondar, Ethiopia
| | - Abayneh G Demisse
- Department of Pediatrics and Child Health, School of Medicine, University of Gondar, Gondar, Ethiopia
| | - Rajashree Mishra
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Tanwi Vartak
- Blizard Institute, Queen Mary University of London, London, UK
| | - Diana L Cousminer
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenyaita M Hodge
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin F Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kim Lorenz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Samuel T Jerram
- Blizard Institute, Queen Mary University of London, London, UK
| | - Arla Gamper
- Severn Postgraduate School of Primary Care, Health Education England, Bristol, UK
| | - Alice Holmes
- Avon and Wiltshire Mental Health Partnership NHS Trust, Clevedon, UK
| | - Hannah F Wilson
- Diabetes and Metabolism, Translational Health Sciences, University of Bristol, Southmead Hospital, Bristol, UK
| | - Alistair J K Williams
- Diabetes and Metabolism, Translational Health Sciences, University of Bristol, Southmead Hospital, Bristol, UK
| | - Struan F A Grant
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R David Leslie
- Blizard Institute, Queen Mary University of London, London, UK
| | - David I W Phillips
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Elisabeth R Trimble
- Centre for Public Health, Institute of Clinical Science, Queen's University Belfast, Grosvenor Road, Belfast, BT12 6BA, UK.
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25
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Beigmohammadi F, Mahmoudi M, Karami J, Ahmadzadeh N, Ebrahimi-Daryani N, Rezaei N. Analysis of Killer Cell Immunoglobulin-Like Receptor Genes and Their HLA Ligands in Inflammatory Bowel Diseases. J Immunol Res 2020; 2020:4873648. [PMID: 33015197 PMCID: PMC7520679 DOI: 10.1155/2020/4873648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/16/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic studies have illustrated that killer cell immunoglobulin-like receptor (KIR) genes could participate in various autoimmune disorders. We aimed to clarify the role of KIR genes, HLA ligands, HLA-KIR interactions, and their genotypes in inflammatory bowel disease (IBD) susceptibility. The study population was composed of 183 IBD subjects, comprising 100 ulcerative colitis (UC) patients, 83 Crohn's disease (CD) patients, and 274 healthy subjects. Polymerase chain reaction with sequence-specific primers (PCR-SSP) was used to evaluate the absence or presence of the 15 KIR genes, 5 HLA class I ligands, and 2 pseudogenes. We did not find any significant difference in allele frequency of KIRs and pseudogenes between IBD patients and healthy controls. In the case of HLA genes, there was a significant difference in HLA-B-Bw4Thr80 frequency between UC patients and healthy controls (P = 0.03, OR = 0.06, 95%CI = 0.008-0.4). Furthermore, we found a significant difference in HLA-C1Asn80 frequency between CD patients and healthy controls (P = 0.04, OR = 0.49, 95% CI = 0.3-0.8). In the full-array combination of KIR genes, there was no significant frequency difference between UC patients and healthy controls, while two KIR genotypes showed a significant susceptible association with CD. Our data do not support a strong role of NK cells in IBD susceptibility, but it does not rule out a role for KIR variability in IBD patients. However, there are some protective associations such as Bw4 alleles; these associations may be due to the interaction of the alleles to TCRs rather than KIRs.
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Affiliation(s)
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Rheumatology Expert Group (REG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jafar Karami
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nooshin Ahmadzadeh
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nasser Ebrahimi-Daryani
- Department of Gastroenterology and Hepatology, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
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26
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Vargas LDB, Dourado RM, Amorim LM, Ho B, Calonga-Solís V, Issler HC, Marin WM, Beltrame MH, Petzl-Erler ML, Hollenbach JA, Augusto DG. Single Nucleotide Polymorphism in KIR2DL1 Is Associated With HLA-C Expression in Global Populations. Front Immunol 2020; 11:1881. [PMID: 32983108 PMCID: PMC7478174 DOI: 10.3389/fimmu.2020.01881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Regulation of NK cell activity is mediated through killer-cell immunoglobulin-like receptors (KIR) ability to recognize human leukocyte antigen (HLA) class I molecules as ligands. Interaction of KIR and HLA is implicated in viral infections, autoimmunity, and reproduction and there is growing evidence of the coevolution of these two independently segregating gene families. By leveraging KIR and HLA-C data from 1000 Genomes consortium we observed that the KIR2DL1 variant rs2304224 * T is associated with lower expression of HLA-C in individuals carrying the ligand HLA-C2 (p = 0.0059). Using flow cytometry, we demonstrated that this variant is also associated with higher expression of KIR2DL1 on the NK cell surface (p = 0.0002). Next, we applied next generation sequencing to analyze KIR2DL1 sequence variation in 109 Euro and 75 Japanese descendants. Analyzing the extended haplotype homozygosity, we show signals of positive selection for rs4806553 * G and rs687000 * G, which are in linkage disequilibrium with rs2304224 * T. Our results suggest that lower expression of HLA-C2 ligands might be compensated for higher expression of the receptor KIR2DL1 and bring new insights into the coevolution of KIR and HLA.
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Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Renata M Dourado
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Leonardo M Amorim
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Brenda Ho
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Verónica Calonga-Solís
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Hellen C Issler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
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27
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Parry HM, Mirajkar N, Cutmore N, Zuo J, Long H, Kwok M, Oldrieve C, Hudson C, Stankovic T, Paneesha S, Kelly M, Begum J, McSkeane T, Pratt G, Moss P. Long-Term Ibrutinib Therapy Reverses CD8 + T Cell Exhaustion in B Cell Chronic Lymphocytic Leukaemia. Front Immunol 2019; 10:2832. [PMID: 31921116 PMCID: PMC6921985 DOI: 10.3389/fimmu.2019.02832] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
Chronic Lymphocytic Leukaemia (CLL) is associated with immune suppression and susceptibility to infection. CD8+ T cell numbers are increased and demonstrate elevated expression of PD-1 and impaired function. The mechanisms driving these features of exhaustion are uncertain but are likely to include chronic immune recognition of tumor and/or infectious agents. We investigated the number, phenotype and function of total and virus-specific CD8+ T cells in 65 patients with CLL and 14 patients undergoing long-term ibrutinib therapy (median 21 months). Ibrutinib substantially reduced the number of both CD3+ T cells and CD8+ T cells. Importantly, this was associated with a reduction in PD-1 expression on CD8+ T cells (median 28 vs. 24%; p = 0.042) and 3.5 fold increase in cytokine production following mitogen stimulation. The influence of ibrutinib on antigen-specific CD8+ T cell function was assessed by HLA-peptide tetramers and revealed increased IFNγ and TNFα cytokine responses following stimulation with CMV or EBV peptides together with a 55% reduction in the frequency of "inflated" virus-specific CD8+ T cells. These findings reveal that long-term ibrutinib therapy is associated with substantial reversal of T cell exhaustion in B-CLL and is likely to contribute to the reduced infection risk seen in association with this agent.
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MESH Headings
- Adenine/analogs & derivatives
- Aged
- Biomarkers
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/pathology
- Cytomegalovirus/immunology
- Duration of Therapy
- Female
- Herpesvirus 4, Human/immunology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Middle Aged
- Peptides/immunology
- Piperidines
- Protein Kinase Inhibitors/administration & dosage
- Protein Kinase Inhibitors/adverse effects
- Protein Kinase Inhibitors/therapeutic use
- Pyrazoles/administration & dosage
- Pyrazoles/adverse effects
- Pyrazoles/therapeutic use
- Pyrimidines/administration & dosage
- Pyrimidines/adverse effects
- Pyrimidines/therapeutic use
- Treatment Outcome
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Affiliation(s)
- Helen M. Parry
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Nikhil Mirajkar
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Natasha Cutmore
- St James' University Hospital, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
| | - Jianmin Zuo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Heather Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Marwan Kwok
- Institute of Cancer and Genomic Sciences University of Birmingham, Birmingham, United Kingdom
| | - Ceri Oldrieve
- Institute of Cancer and Genomic Sciences University of Birmingham, Birmingham, United Kingdom
| | - Chris Hudson
- Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences University of Birmingham, Birmingham, United Kingdom
| | - Shankara Paneesha
- Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Melanie Kelly
- Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Jusnara Begum
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Tina McSkeane
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
| | - Guy Pratt
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Paul Moss
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
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Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice. G3-GENES GENOMES GENETICS 2019; 9:4223-4233. [PMID: 31645420 PMCID: PMC6893195 DOI: 10.1534/g3.119.400740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetic mapping is a primary tool of genetics in model organisms; however, many quantitative trait loci (QTL) contain tens or hundreds of positional candidate genes. Prioritizing these genes for validation is often ad hoc and biased by previous findings. Here we present a technique for prioritizing positional candidates based on computationally inferred gene function. Our method uses machine learning with functional genomic networks, whose links encode functional associations among genes, to identify network-based signatures of functional association to a trait of interest. We demonstrate the method by functionally ranking positional candidates in a large locus on mouse Chr 6 (45.9 Mb to 127.8 Mb) associated with histamine hypersensitivity (Histh). Histh is characterized by systemic vascular leakage and edema in response to histamine challenge, which can lead to multiple organ failure and death. Although Histh risk is strongly influenced by genetics, little is known about its underlying molecular or genetic causes, due to genetic and physiological complexity of the trait. To dissect this complexity, we ranked genes in the Histh locus by predicting functional association with multiple Histh-related processes. We integrated these predictions with new single nucleotide polymorphism (SNP) association data derived from a survey of 23 inbred mouse strains and congenic mapping data. The top-ranked genes included Cxcl12, Ret, Cacna1c, and Cntn3, all of which had strong functional associations and were proximal to SNPs segregating with Histh. These results demonstrate the power of network-based computational methods to nominate highly plausible quantitative trait genes even in challenging cases involving large QTL and extreme trait complexity.
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Wang Y, Zhang T, Zhang L, Pei Y, Zhao L, Li Y, Liu L, Wang H. Development of a rapid and reliable single-tube multiplex real-time PCR method for HLA-A*24:02 genotyping. Pharmacogenomics 2019; 20:803-812. [PMID: 31368852 DOI: 10.2217/pgs-2019-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aim: HLA-A*24:02 is significantly associated with cutaneous adverse drug reactions caused by aromatic antiepileptic drugs. Here, we aimed to establish a fast and reliable detection method for HLA-A*24:02 genotyping. Methods: A single-tube multiplex quantitative real-time polymerase chain reaction (qPCR) assay for HLA-A*24:02 genotyping was established by combining allele-specific primers with TaqMan probes. Results: A 100% concordance was observed between qPCR and SBT result in 106 Han subjects. The detection limit of the new method was 0.05 ng DNA. The positive rate of HLA-A*24:02 in Tibetans (55.6%, n = 81) was significantly higher than those in Han (34%, n = 106), Uighur (27.5%, n = 102), Bouyei (25.9%, n = 116) and Miao populations (26.5%, n = 113). Conclusion: The newly established qPCR assay was reliable for HLA-A*24:02 screening in clinical applications.
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Affiliation(s)
- Yanxia Wang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Tingting Zhang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Lirong Zhang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Yanrui Pei
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Lili Zhao
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Yanwei Li
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
| | - Lin Liu
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Huijuan Wang
- School of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China.,National Engineering Research Center for Miniaturized Detection Systems, Xi'an 710069, PR China
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30
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Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population. Hum Immunol 2019; 80:807-822. [PMID: 31345698 DOI: 10.1016/j.humimm.2019.07.275] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 06/21/2019] [Accepted: 07/06/2019] [Indexed: 12/11/2022]
Abstract
The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the technology used to characterize HLA alleles; high-resolution genotyping of long-range HLA gene products improves the assessment of HLA population diversity as well as other population parameters compared to lower resolution typing methods. In this study we examined allelic and haplotype HLA diversity in a large healthy European American population sourced from the UCSF-DNA bank. A high-resolution next-generation sequencing method was applied to define non-ambiguous 3- and 4-field alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 loci in samples provided by 2248 unrelated individuals. A number of population parameters were examined including balancing selection and various measurements of linkage disequilibrium were calculated. There were no detectable deviations from Hardy-Weinberg proportions at HLA-A, HLA-DRB1, HLA-DQA1 and HLA-DQB1. For the remaining loci moderate and significant deviations were detected at HLA-C, HLA-B, HLA-DRB3/4/5, HLA-DPA1 and HLA-DPB1 loci mostly from population substructures. Unique 4-field associations were observed among alleles at 2 loci and haplotypes extending large intervals that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. The high diversity at HLA-DPA1 results from detection of intron variants of otherwise well conserved protein sequences. It may be speculated that divergence in exon sequences may be negatively selected. Our data provides a valuable reference source for future population studies that may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity.
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31
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Binks S, Varley J, Lee W, Makuch M, Elliott K, Gelfand JM, Jacob S, Leite MI, Maddison P, Chen M, Geschwind MD, Grant E, Sen A, Waters P, McCormack M, Cavalleri GL, Barnardo M, Knight JC, Irani SR. Distinct HLA associations of LGI1 and CASPR2-antibody diseases. Brain 2019; 141:2263-2271. [PMID: 29788256 PMCID: PMC6118231 DOI: 10.1093/brain/awy109] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/09/2018] [Indexed: 01/17/2023] Open
Abstract
The recent biochemical distinction between antibodies against leucine-rich, glioma-inactivated-1 (LGI1), contactin-associated protein-2 (CASPR2) and intracellular epitopes of voltage-gated potassium-channels (VGKCs) demands aetiological explanations. Given established associations between human leucocyte antigen (HLA) alleles and adverse drug reactions, and our clinical observation of frequent adverse drugs reactions in patients with LGI1 antibodies, we compared HLA alleles between healthy controls (n = 5553) and 111 Caucasian patients with VGKC-complex autoantibodies. In patients with LGI1 antibodies (n = 68), HLA-DRB1*07:01 was strongly represented [odds ratio = 27.6 (95% confidence interval 12.9–72.2), P = 4.1 × 10−26]. In contrast, patients with CASPR2 antibodies (n = 31) showed over-representation of HLA-DRB1*11:01 [odds ratio = 9.4 (95% confidence interval 4.6–19.3), P = 5.7 × 10−6]. Other allelic associations for patients with LGI1 antibodies reflected linkage, and significant haplotypic associations included HLA-DRB1*07:01-DQA1*02:01-DQB1*02:02, by comparison to DRB1*11:01-DQA1*05:01-DQB1*03:01 in CASPR2-antibody patients. Conditional analysis in LGI1-antibody patients resolved further independent class I and II associations. By comparison, patients with both LGI1 and CASPR2 antibodies (n = 3) carried yet another complement of HLA variants, and patients with intracellular VGKC antibodies (n = 9) lacked significant HLA associations. Within LGI1- or CASPR2-antibody patients, HLA associations did not correlate with clinical features. In silico predictions identified unique CASPR2- and LGI1-derived peptides potentially presented by the respective over-represented HLA molecules. These highly significant HLA associations dichotomize the underlying immunology in patients with LGI1 or CASPR2 antibodies, and inform T cell specificities and cellular interactions at disease initiation.
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Affiliation(s)
- Sophie Binks
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - James Varley
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Wanseon Lee
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Mateusz Makuch
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Katherine Elliott
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jeffrey M Gelfand
- UCSF Department of Neurology, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Saiju Jacob
- Centre for Rare Diseases and Queen Elizabeth Neuroscience Centre, University Hospitals Birmingham, UK
| | - M Isabel Leite
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Paul Maddison
- Department of Neurology, Queen's Medical Centre, Derby Road, Nottingham NG7 2UH, UK
| | - Mian Chen
- Transplant Immunology and Immunogenetics Laboratory, Oxford Transplant Centre, Churchill Hospital, Oxford, UK
| | - Michael D Geschwind
- UCSF Department of Neurology, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Eleanor Grant
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Arjune Sen
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Patrick Waters
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Mark McCormack
- Department of Molecular and Cellular Therapeutics, the Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, the Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Martin Barnardo
- Transplant Immunology and Immunogenetics Laboratory, Oxford Transplant Centre, Churchill Hospital, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 3, West Wing, John Radcliffe Hospital, Oxford, OX3 9DS, UK
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32
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Çebi M, Durmuş H, Yılmaz V, Yentür SP, Aysal F, Oflazer P, Parman Y, Deymeer F, Saruhan-Direskeneli G. Relation of HLA-DRB1 to IgG4 autoantibody and cytokine production in muscle-specific tyrosine kinase myasthenia gravis (MuSK-MG). Clin Exp Immunol 2019; 197:214-221. [PMID: 30929252 DOI: 10.1111/cei.13302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
A small subset of myasthenia gravis (MG) patients develop autoantibodies against muscle-specific kinase (MuSK), which are predominantly of the immunoglobulin (Ig)G4 isotype. MuSK-MG is strongly associated with HLA-DRB1*14, HLA-DRB1*16 and HLA-DQB1*05. In this study, the possible effects of these HLA associations on MuSK IgG autoantibody or cytokine production were investigated. Samples from 80 MG patients with MuSK antibodies were studied. The disease-associated HLA types were screened in the DNA samples. The IgG1, IgG2, IgG3 and IgG4 titres of the MuSK antibodies and the levels of interleukin (IL)-4, IL-6, IL-17A and IL-10 were measured in the sera. Comparisons were made among the groups with or without HLA-DRB1*14, HLA-DRB1*16 or HLA-DQB1*05. The IgG4 titres of the MuSK antibodies were higher than those of the IgG1, IgG2 and IgG3 isotypes among the whole group of patients. DRB1*14 (+) DRB1*16 (-) patients had higher levels of IgG4 antibodies than those of DRB1*14 (-) DRB1*16 (+) patients. DRB1*14 (+) DRB1*16 (+) patients also had higher levels of IgG4 antibodies than those of DRB1*14 (-) DRB1*16 (+) and DRB1*14 (-) DRB1*16 (-) patients. Higher IL-10 and lower IL-17A levels were measured in DRB1*14 (+) DRB1*16 (-) patients than in DRB1*14 (-) DRB1*16 (-) patients. The higher IgG4 titres of MuSK autoantibodies in patients carrying HLA-DRB1*14 than those in the other patients suggest a role for HLA in the production of the antibodies. The differences in IL-10 and IL-17A support the role of DRB1 in the etiopathogenesis of this autoimmune response.
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Affiliation(s)
- M Çebi
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - H Durmuş
- Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - V Yılmaz
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - S P Yentür
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - F Aysal
- Department of Neurology, Bakirkoy Research and Training Hospital for Psychiatric and Neurological Diseases, Istanbul, Turkey.,Department of Neurology, Istanbul Medipol University School of Medicine, Istanbul, Turkey
| | - P Oflazer
- Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Y Parman
- Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - F Deymeer
- Department of Neurology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - G Saruhan-Direskeneli
- Department of Physiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
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33
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Telomere shortening in blood leukocytes of patients with posttraumatic stress disorder. J Psychiatr Res 2019; 111:83-88. [PMID: 30685566 DOI: 10.1016/j.jpsychires.2019.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/14/2019] [Accepted: 01/21/2019] [Indexed: 01/09/2023]
Abstract
Telomeres are protective fragments on chromosome ends involved in maintaining genome stability, preventing chromosomal fusions, regulation of cell division. It was shown that telomere attrition rate is accelerated in age-related diseases, as well as in response to physiological and psychosocial stress. The aim of this study was to evaluate relative leukocyte telomere length (LTL) in patients with post traumatic stress disorder (PTSD), as well as to investigate association of functional SNPs of telomerase TERC and TERT genes with LTL and PTSD. The relative LTL was measured by multiplex quantitative PCR method; genotyping of TERC rs12696304, TERT rs7726159 and rs2736100 was performed by PCR with sequence specific primers. Comparison of LTL in diseased and healthy subjects showed that PTSD patients had shorter average LTL than controls. Also, the frequency and the carriage rate of the TERT rs2736100*T allele was higher in PTSD patients compared to controls. Overall our results are in line with previous research in different populations. Furthermore, we have demonstrated that rs2736100 of TERT gene was significantly associated with PTSD and the minor allele of this polymorphism may be considered as a risk factor for PTSD in the Armenian population.
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Creary LE, Guerra SG, Chong W, Brown CJ, Turner TR, Robinson J, Bultitude WP, Mayor NP, Marsh SGE, Saito K, Lam K, Duke JL, Mosbruger TL, Ferriola D, Monos D, Willis A, Askar M, Fischer G, Saw CL, Ragoussis J, Petrek M, Serra-Pagés C, Juan M, Stavropoulos-Giokas C, Dinou A, Ameen R, Al Shemmari S, Spierings E, Gendzekhadze K, Morris GP, Zhang Q, Kashi Z, Hsu S, Gangavarapu S, Mallempati KC, Yamamoto F, Osoegawa K, Vayntrub T, Chang CJ, Hansen JA, Fernández-Viňa MA. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop. Hum Immunol 2019; 80:449-460. [PMID: 30844424 DOI: 10.1016/j.humimm.2019.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/09/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Sandra G Guerra
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK
| | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Will P Bultitude
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Katsuyuki Saito
- Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA
| | - Kevin Lam
- Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA
| | - Jamie L Duke
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy L Mosbruger
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Deborah Ferriola
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dimitrios Monos
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Lab Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA
| | - Gottfried Fischer
- Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Chee Loong Saw
- HLA Laboratory, Division of Haematology, McGill University Health Centre, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University & McGill University and Genome Quèbec Innovation Centre, Montreal, Canada
| | - Martin Petrek
- Department of Pathological Physiology and Immunogenomics, IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Carles Serra-Pagés
- Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Manel Juan
- Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | | | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | - Reem Ameen
- Health Sciences Center, Kuwait University, Kuwait
| | | | - Eric Spierings
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, Netherlands
| | | | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Qiuheng Zhang
- Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA
| | - Zahra Kashi
- HLA Department, Kashi Clinical Laboratories, Inc., Portland, OR, USA
| | - Susan Hsu
- HLA Laboratory, American Red Cross, Philadelphia, PA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Fumiko Yamamoto
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Tamara Vayntrub
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | | | - John A Hansen
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marcelo A Fernández-Viňa
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
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Law SC, Haigh OL, Walpole CM, Keane C, Miles JJ, Gandhi MK, Radford KJ, Steptoe RJ. Simple, rapid and inexpensive typing of common HLA class I alleles for immunological studies. J Immunol Methods 2018; 465:72-76. [PMID: 30537479 DOI: 10.1016/j.jim.2018.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 12/22/2022]
Abstract
Current HLA-typing methods are typically designed to provide exquisitely-detailed identification of multiple HLA-alleles to satisfy the requirements for organ and bone marrow transplantation or genetic studies. Many human immunological studies, on the other hand, focus around only a small number of HLA alleles that are abundant or of relevance to specific diseases. Consequently, for such studies, many HLA typing approaches are not cost-effective and are potentially complicated, slow and not easily performed in-house. Work-flow would be streamlined by a simple, inexpensive and rapid typing method able to be performed in-house. We outline a straightforward approach that provides appropriate data for much immunological research. In a predominantly Caucasian population, flow cytometry using anti-HLA-A2, -B8 and -B7 antibodies consistently and accurately screened for samples carrying the highly-abundant HLA class I alleles HLA-A*02:01, -B*08:01 and -B*07:02 that form the focus of immunological studies. Next, we describe a straightforward and simple strategy for design and use of allele-specific PCR primers to identify, at high-resolution, alleles of interest. When combined with a simple gDNA extraction technique this provides reliable, simple and inexpensive in-house HLA typing demonstrated here for highly-abundant HLA class I alleles.
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Affiliation(s)
- Soi Cheng Law
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Oscar L Haigh
- Mater Research UQ, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Carina M Walpole
- Mater Research UQ, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Colm Keane
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - John J Miles
- Australian Institute of Tropical Medicine & Health, James Cook University, Cairns, Queensland, Australia
| | - Maher K Gandhi
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Kristen J Radford
- Mater Research UQ, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Raymond J Steptoe
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.
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Guan L, Li X, Wei J, Liang Z, Yang J, Weng X, Wu X. Antigen-specific CD8+ memory stem T cells generated from human peripheral blood effectively eradicate allogeneic targets in mice. Stem Cell Res Ther 2018; 9:337. [PMID: 30526661 PMCID: PMC6286512 DOI: 10.1186/s13287-018-1080-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND As the implantation and long-term existence of tumor-specific T cells in host are the prerequisite for adoptive immunotherapy, memory stem T cells (TSCM) with self-renewal and differentiation capacity show the greatest potential to implant and long-term exhibit function in vivo, compared with other T cells of differentiation stages. Hence, tumor-specific TSCM have become potential candidate for adoptive T cell therapy of cancer. Here, we reported a protocol to generate allogeneic antigen-specific CD8+ TSCM cells from human PBLs. METHODS To prepare allogeneic antigen-specific CD8+ TSCM, we used an LCL named E007 of defined HLA allotyping as simulator, a co-culture of E007 and allogeneic PBLs was carried out in the presence of differentiation inhibitor TWS119 for 7 days. Sorting of proliferation cells ensured the E007-specificity of the prepared TSCM cells. The sorted lymphocytes underwent further expansion by cytokines IL-7 and IL-15 for further 7 days, making the E007-specific CD8 + TSCM expanded in number. The stem cell and T memory cell properties of the prepared CD8+ TSCM were observed in NOD-SCID mice. RESULTS Our protocol began with 1 × 107 PBLs and resulted in 2 × 107 E007-specific CD8+ TSCM cells in 2 weeks of preparation. The prepared TSCM cells exhibited a proliferative history and rapid differentiation into effector cells upon the E007 re-stimulation. Importantly, the prepared TSCM cells were able to exist long and reconstitute other T cell subsets in vivo, eradicating the E007 cells effectively after transferred into the LCL burden mice. CONCLUSIONS This protocol was able to prepare allogeneic antigen-specific CD8+ TSCM cells from human PBLs. The prepared TSCM showed the properties of stem cells and T memory cells. This study provided a reference method for generation of antigen-specific TSCM for T cell adoptive immunotherapy.
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Affiliation(s)
- Liping Guan
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China
| | - Xiaoyi Li
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China
| | - Jiali Wei
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China
| | - Zhihui Liang
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China
| | - Jing Yang
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China
| | - Xiufang Weng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China.
| | - Xiongwen Wu
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, China.
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Madden K, Chabot-Richards D. HLA testing in the molecular diagnostic laboratory. Virchows Arch 2018; 474:139-147. [PMID: 30515565 DOI: 10.1007/s00428-018-2501-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/27/2018] [Indexed: 02/06/2023]
Abstract
The human leukocyte antigen (HLA) system is a highly polymorphic family of genes involved in immunity and responsible for identifying self versus non-self. HLA typing is essential for solid organ and bone marrow transplantation as well as in non-transplant settings such as disease association and pharmacogenomics. Typing of HLA genes differs from most molecular testing as, rather than evaluating differences from an accepted "wild-type" gene, it must distinguish between thousands of similar, but distinct alleles. This article will describe the HLA system and nomenclature. We will then discuss clinical uses of HLA typing including solid organ transplantation, hematopoietic stem cell transplantation, evaluation of platelet refractory patients, disease association, and pharmacogenetics. Finally, we describe common molecular methods of HLA typing.
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Affiliation(s)
- Kathleen Madden
- Department of Pathology, University of New Mexico, MSC08 4640, Reginald Heber Fitz Hall, Room 335, 1 University of New Mexico, 87131, Albuquerque, NM, Mexico
| | - Devon Chabot-Richards
- Department of Pathology, University of New Mexico, MSC08 4640, Reginald Heber Fitz Hall, Room 335, 1 University of New Mexico, 87131, Albuquerque, NM, Mexico.
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Zipeto D, Serena M, Mutascio S, Parolini F, Diani E, Guizzardi E, Muraro V, Lattuada E, Rizzardo S, Malena M, Lanzafame M, Malerba G, Romanelli MG, Tamburin S, Gibellini D. HIV-1-Associated Neurocognitive Disorders: Is HLA-C Binding Stability to β 2-Microglobulin a Missing Piece of the Pathogenetic Puzzle? Front Neurol 2018; 9:791. [PMID: 30298049 PMCID: PMC6160745 DOI: 10.3389/fneur.2018.00791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/03/2018] [Indexed: 01/09/2023] Open
Abstract
AIDS dementia complex (ADC) and HIV-associated neurocognitive disorders (HAND) are complications of HIV-1 infection. Viral infections are risk factors for the development of neurodegenerative disorders. Aging is associated with low-grade inflammation in the brain, i.e., the inflammaging. The molecular mechanisms linking immunosenescence, inflammaging and the pathogenesis of neurodegenerative disorders, such as Alzheimer's disease (AD) and Parkinson's disease, are largely unknown. ADC and HAND share some pathological features with AD and may offer some hints on the relationship between viral infections, neuroinflammation, and neurodegeneration. β2-microglobulin (β2m) is an important pro-aging factor that interferes with neurogenesis and worsens cognitive functions. Several studies published in the 80-90s reported high levels of β2m in the cerebrospinal fluid of patients with ADC. High levels of β2m have also been detected in AD. Inflammatory diseases in elderly people are associated with polymorphisms of the MHC-I locus encoding HLA molecules that, by associating with β2m, contribute to cellular immunity. We recently reported that HLA-C, no longer associated with β2m, is incorporated into HIV-1 virions, determining an increase in viral infectivity. We also documented the presence of HLA-C variants more or less stably linked to β2m. These observations led us to hypothesize that some variants of HLA-C, in the presence of viral infections, could determine a greater release and accumulation of β2m, which in turn, may be involved in triggering and/or sustaining neuroinflammation. ADC is the most severe form of HAND. To explore the role of HLA-C in ADC pathogenesis, we analyzed the frequency of HLA-C variants with unstable binding to β2m in a group of patients with ADC. We found a higher frequency of unstable HLA-C alleles in ADC patients, and none of them was harboring stable HLA-C alleles in homozygosis. Our data suggest that the role of HLA-C variants in ADC/HAND pathogenesis deserves further studies. If confirmed in a larger number of samples, this finding may have practical implication for a personalized medicine approach and for developing new therapies to prevent HAND. The exploration of HLA-C variants as risk factors for AD and other neurodegenerative disorders may be a promising field of study.
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Affiliation(s)
- Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Michela Serena
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Simona Mutascio
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Francesca Parolini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Erica Diani
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | | | | | | | | | - Marina Malena
- U.O.S. Infectious Diseases, AULSS 9 Scaligera, Verona, Italy
| | | | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Maria Grazia Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Stefano Tamburin
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Davide Gibellini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
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Hu S, Yuan F, Feng L, Zheng F, Gong F, Huang H, Sun B. KIR2DL2/C1 is a Risk Factor for Chronic Infection and Associated with Non-response to PEG-IFN and RBV Combination Therapy in Hepatitis C Virus Genotype 1b Patients in China. Virol Sin 2018; 33:369-372. [PMID: 30039498 DOI: 10.1007/s12250-018-0042-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- Song Hu
- Medical College, Jianghan University, Wuhan, 430056, China
| | - Fahu Yuan
- Medical College, Jianghan University, Wuhan, 430056, China
| | - Lingyan Feng
- Medical College, Jianghan University, Wuhan, 430056, China
| | - Fang Zheng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Feili Gong
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hanju Huang
- Department of Pathogen Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Binlian Sun
- Medical College, Jianghan University, Wuhan, 430056, China.
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Sun HS, Liu DX, Bai YY, Hu NW. Disease-association of different killer cell immunoglobulin-like receptors (KIR) and HLA-C gene combinations in reactive arthritis. Mod Rheumatol 2018; 29:531-537. [PMID: 29848119 DOI: 10.1080/14397595.2018.1483292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hong Sheng Sun
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Dong Xia Liu
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Yan Yan Bai
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Nai Wen Hu
- Department of Rheumatology and Immunology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
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Murad H, Jazairi B, Khansaa I, Olabi D, Khouri L. HLA-DQ2 and -DQ8 genotype frequency in Syrian celiac disease children: HLA-DQ relative risks evaluation. BMC Gastroenterol 2018; 18:70. [PMID: 29793442 PMCID: PMC5968552 DOI: 10.1186/s12876-018-0802-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/16/2018] [Indexed: 12/11/2022] Open
Abstract
Background Celiac disease (CD) is a common autoimmune disease in Syria which manifesting with inflammation of the small intestine and with various extra intestinal symptoms. The disease is associated with human HLA-DQ genes encoding HLA-DQ2 and DQ8 proteins. Methods In this study, 49 children patients of CD and 58 healthy control samples were genotyped for HLA-DQ genes using SSP-PCR technique. Relative risks for different genotypes were also evaluated. Results The DQB1*0201 allele was the most common in the patients (77.6%) followed by DQB1*0302 allele (10.2%). The highest HLA-DQB risk for CD development was found in patients carriers a DQ2.5/DQ8 genotype (1/10), followed by the patients carriers DQ2.5/DQ2.5 (1/12). Conclusion The significant differences in the frequency of HLA-DQ2 and HLA-DQ8 in Syrian patients in compared with controls and relative risks predicted demonstrated the importance role of these alleles in the development of CD in Syrian children patients.
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Affiliation(s)
- Hossam Murad
- Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria.
| | - Batoul Jazairi
- Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | - Issam Khansaa
- Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
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Adams SD, Barracchini KC, Simonis TB, Stroncek D, Marincola FM. High Throughput Hla Sequence-Based Typing (Sbt) Utilizing the Abi Prism® 3700 Dna Analyzer. TUMORI JOURNAL 2018. [DOI: 10.1177/030089160108700228] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Aims and background The genetic complexity of the human major histocompatibility complex (MHC) has required the development of various molecular typing methods. The purpose of this paper is to compare the results of two of these molecular methods: sequenced based typing (SBT) and polymerase chain reaction (PCR) using sequence specific primers (PCR-SSP). Methods The SBT method described utilizes an ABI Prism® 3700 DNA Analyzer, which has been designed fro high throughput production of sequence data through highly automated operation with significant walk-away time. The ABI Prism® 3700 DNA Analyzer is a 96-capillary electrophoresis instrument with the capability of running four 96-well plates black to back in a sixteen-hour period. Potentially, data from this machine can produce Class I sequences for A or B loci for 64 samples in this time frame. The SBT method encompassed exons 2, 3, and 4 with forward and reverse sequence orientation reactions using the PE Biosystems HLA-A and HLA-B Sequenced Based Typing Kits (PE Applied Biopsystems/Perkin-Elmer, Foster City, CA, USA). Most SBT methods previously employed only gather data from exons 2 and 3 which distinguishes most of the polymorphism necessary to identify the majority of alleles in the HLA region. However, in an effort to discern numerous null alleles in the HLA region, exon 4 data is also included. The PCR-SSP method utilized consists of one 96 well tray, with 95 primer mixes and one negative control, per sample designed to produce an intermediate/high resolution HLA-A, B typing. Results Data from one 96-well capillary run on the ABI Prism® 3700 DNA Analyzer, which consists of results from 16 samples for HLA-A or HLA-B loci, was compared to data derived from sixteen HLA-A and HLA-B PCR-SSP typings. 75% of loci tested achieved a higher resolution HLA typing by the SBT method. Discussion The ability to provide allele level HLA typing results can have significant functional implications for the bone marrow transplant community and numerous vaccine studies.
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Affiliation(s)
- Sharon D Adams
- HLA Laboratory, Department of Transfusion Medicine, Warren G Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Kathleen C Barracchini
- HLA Laboratory, Department of Transfusion Medicine, Warren G Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Toni B Simonis
- HLA Laboratory, Department of Transfusion Medicine, Warren G Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - David Stroncek
- HLA Laboratory, Department of Transfusion Medicine, Warren G Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Francesco M Marincola
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Seiffert-Sinha K, Khan S, Attwood K, Gerlach JA, Sinha AA. Anti-Thyroid Peroxidase Reactivity Is Heightened in Pemphigus Vulgaris and Is Driven by Human Leukocyte Antigen Status and the Absence of Desmoglein Reactivity. Front Immunol 2018; 9:625. [PMID: 29675021 PMCID: PMC5896579 DOI: 10.3389/fimmu.2018.00625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/13/2018] [Indexed: 12/17/2022] Open
Abstract
Pemphigus vulgaris (PV) belongs to an autoimmune disease cluster that includes autoimmune thyroid disease (AITD), suggesting common mechanisms driving autoimmune susceptibility. Our group has shown that PV patients exhibit significant reactivity to AITD-related anti-thyroid peroxidase (anti-TPO), and anti-TPO antibodies affect signaling pathways in keratinocytes similar to anti-desmoglein (Dsg) 3 antibodies. To further assess the relevance of anti-TPO reactivity in PV, we analyzed anti-TPO levels in 280 PV and 167 healthy control serum samples across a comprehensive set of variable and static parameters of disease activity and etiopathogenesis. PV patients have significantly higher activity rates (A.R.s) for anti-TPO than healthy controls, but levels do not differ between phases of clinical activity and remission. Patients that carry both the PV-associated human leukocyte antigen (HLA) alleles DRB1*0402 and DQB1*0503, or DQB1*0503 alone show a low prevalence of anti-TPO (A.R. 9.5 and 4.8%, respectively), while patients that lack expression of these alleles or carry DRB1*0402 alone have a much higher prevalence of anti-TPO (A.R. 23.1 and 15.8%, respectively), suggesting that the absence of DQB1*0503 may predispose patients to the development of anti-TPO antibodies. Similarly, anti-Dsg1−/3− patients have a higher anti-TPO A.R. (26.9%) than anti-Dsg1−/3+ (18.8%), anti-Dsg1+/3− (14.3%), and anti-Dsg1+/3+ (3.9%) patients. Our data suggest that anti-TPO reactivity in PV is driven by genetic markers that may be in linkage disequilibrium with the established PV-susceptibility alleles and that this association drives the selection of a combination of anti-Dsg and anti-TPO antibodies, with anti-TPO filling the gap in active patients that do not carry the established PV-associated autoantibodies and/or are lacking the established PV-HLA-susceptibility alleles.
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Affiliation(s)
- Kristina Seiffert-Sinha
- Department of Dermatology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
| | - Shahzaib Khan
- Department of Dermatology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
| | - Kristopher Attwood
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - John A Gerlach
- Biomedical Laboratory Diagnostics Program, Tissue Typing Laboratory, Michigan State University, East Lansing, MI, United States
| | - Animesh A Sinha
- Department of Dermatology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
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Gil BC, Kulzer ASS, de Moraes P, Toresan R, da Rosa Vicari A, Dos Santos Fagundes I, Merzoni J, Ewald GM, Cardone JM, Silva FG, Manfro RC, Jobim LF. Comparative analysis of two methods to detect donor-specific anti-HLA antibodies after kidney transplant. Transpl Immunol 2018; 49:7-11. [PMID: 29577967 DOI: 10.1016/j.trim.2018.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 11/29/2022]
Abstract
Preformed anti-human leukocyte antigen (HLA) antibodies may be present in the blood of kidney transplant candidates. The production of these antibodies may occur in the post-transplant period, with the possible development of donor-specific antibodies (DSA). Luminex-based tests, such as the single antigen (SA) assay and the Luminex crossmatch (Xm-DSA) assay are the most commonly used tools to detect anti-HLA antibodies, due to their high sensitivity and specificity. This cross-sectional study aimed to compare the findings of two methods for the detection of DSAs after kidney transplant: SA and Xm-DSA. A total of 122 patients who underwent deceased donor kidney transplant at Hospital de Clínicas de Porto Alegre were included. The SA assay detected anti-class I HLA DSAs in 17 patients (13.9%) and anti-class II HLA DSAs in 22 patients (19.6%), whereas the Xm-DSA detected DSAs in 18 patients (14.8%) both against class I and class II antigens. There was agreement between the two methods for class I (kappa = 0.66, p = 0.001) and class II (kappa = 0.54, p = 0.025) antigens. The incidence of DSAs as obtained by the SA assay was 15.57%, and the most prevalent DSAs were those against HLA-DR antigens. Patient survival at 3 years was 92%. The two techniques assessed in this study provide important information on the presence of DSAs and may help in the post-transplant patient monitoring and in immunosuppressive strategy.
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Affiliation(s)
- Beatriz Chamun Gil
- Service of Immunology, Hospital de Clínicas de Porto Alegre, Brazil; Graduate Program in Medicine: Surgical Sciences, UFRGS, Brazil.
| | | | | | - Realdete Toresan
- Service of Immunology, Hospital de Clínicas de Porto Alegre, Brazil
| | | | | | - Jóice Merzoni
- Service of Immunology, Hospital de Clínicas de Porto Alegre, Brazil; Graduate Program in Medicine: Surgical Sciences, UFRGS, Brazil
| | | | | | | | - Roberto Ceratti Manfro
- Service of Nephrology, Hospital de Clínicas de Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, UFRGS, Brazil
| | - Luiz Fernando Jobim
- Service of Immunology, Hospital de Clínicas de Porto Alegre, Brazil; Graduate Program in Medicine: Surgical Sciences, UFRGS, Brazil
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Kraus AU, Penna-Martinez M, Meyer G, Badenhoop K. Vitamin D effects on monocytes' CCL-2, IL6 and CD14 transcription in Addison's disease and HLA susceptibility. J Steroid Biochem Mol Biol 2018; 177:53-58. [PMID: 28765037 DOI: 10.1016/j.jsbmb.2017.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/31/2022]
Abstract
Addison's disease is a rare autoimmune disorder leading to adrenal insufficiency and life-long glucocorticoid dependency. Vitamin D receptor (VDR) polymorphisms and vitamin D deficiency predispose to Addison's disease. Aim of the current study was, to investigate potential anti-inflammatory vitamin D effects on monocytes in Addison's disease, focusing on inflammatory CCL-2 and IL6, as well on monocyte CD14 markers. Addison's disease is genetically linked to distinct HLA susceptibility alleles. Therefore we analyzed, whether HLA genotypes differed for vitamin D effects on monocyte markers. CD14+ monocytes were isolated from Addison's disease patients (AD, n=13) and healthy controls (HC, n=15) and stimulated with 1,25-dihydroxyvitamin D3 and IL1β as an inflammatory stimulant. Cells were processed for mRNA expression of CCL-2, IL6 and CD14 and DNA samples were genotyped for major histocompatibility class (MHC) class II-encoded HLA- DQA1-DQB1 haplotypes. We found a downregulation of CCL-2 after vitamin D treatment in IL1β-stimulated monocytes both from AD patients and HC (AD p<0.001; HC p<0.0001). CD14 expression however, was upregulated in both HC and AD patients after vitamin D treatment (p<0.001, respectively). HC showed higher CD14 transcription level than AD patients after vitamin D treatment (p=0.04). Compared to IL1β-induced inflammation, HC have increased CD14 levels after vitamin D treatment (p<0.001), whereas the IL1β-induced CD14 expression of AD patients' monocytes did not change after vitamin D treatment (p=0.8). AD patients carrying HLA high-risk haplotypes showed an increased CCL-2 expression after IL1β-induced inflammation compared to intermediate-risk HLA carriers (p=0.05). Also HC monocytes' CD14 transcription after IL1β and vitamin D co-stimulation differed according to HLA risk profile. We show that vitamin D can exert anti-inflammatory effects on AD patients' monocytes which may be modulated by HLA risk genotypes.
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Affiliation(s)
- A U Kraus
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Germany.
| | - M Penna-Martinez
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Germany
| | - G Meyer
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Germany
| | - K Badenhoop
- Department of Internal Medicine I, Division of Endocrinology, Diabetes and Metabolism, University Hospital Frankfurt, Germany
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Jiao Y, Li R, Wu C, Ding Y, Liu Y, Jia D, Wang L, Xu X, Zhu J, Zheng M, Jia J. High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq). BMC Genomics 2018; 19:50. [PMID: 29334893 PMCID: PMC5769328 DOI: 10.1186/s12864-018-4431-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/03/2018] [Indexed: 12/04/2022] Open
Abstract
Background Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine. Results Here, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing. Conclusions STC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine. Electronic supplementary material The online version of this article (10.1186/s12864-018-4431-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Jiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Ran Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Chao Wu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Yibin Ding
- School of Mathematical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Yanning Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Danmei Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Lifeng Wang
- Beijing Ming-tian Genetics Ltd, Beijing, 100070, People's Republic of China
| | - Xiang Xu
- School of Mathematical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Jing Zhu
- Beijing Ming-tian Genetics Ltd, Beijing, 100070, People's Republic of China.
| | - Min Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China. .,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China.
| | - Junling Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China. .,Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China.
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Wang E, Adams S, Stroncek DF, Marincola FM. Human Leukocyte Antigen and Human Neutrophil Antigen Systems. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00113-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Hosie L, Pachnio A, Zuo J, Pearce H, Riddell S, Moss P. Cytomegalovirus-Specific T Cells Restricted by HLA-Cw*0702 Increase Markedly with Age and Dominate the CD8 + T-Cell Repertoire in Older People. Front Immunol 2017; 8:1776. [PMID: 29312307 PMCID: PMC5732243 DOI: 10.3389/fimmu.2017.01776] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
Cytomegalovirus (CMV) infection elicits a strong T-cell immune response, which increases further during aging in a process termed "memory inflation." CMV downregulates the expression of HLA-A and HLA-B on the surface of infected cells to limit presentation of viral peptides to T-cells although HLA-C is relatively spared as it also engages with inhibitory killer immunoglobulin receptor receptors and therefore reduces lysis by natural killer cells. We investigated the magnitude and functional properties of CMV-specific CD8+ T-cells specific for 10 peptides restricted by HLA-C in a cohort of 53 donors between the age of 23 and 91 years. This was achieved via peptide stimulation of PBMCs followed by multicolor flow cytometry. Three peptides, derived from proteins generated in the immediate-early period of viral replication and restricted by HLA-Cw*0702, elicited strong immune responses, which increased substantially with age such that the average aggregate response represented 37% of the CD8+ T-cell pool within donors above 70 years of age. Remarkably, a single response represented 70% of the total CD8+ T-cell pool within a 91-year-old donor. HLA-Cw*0702-restricted CD8+ T-cell responses were immunodominant over HLA-A and HLA-B-restricted CMV-specific responses and did not show features of exhaustion such as PD-1 or CD39 expression. Indeed, such CTL exhibit a polyfunctional cytokine profile with co-expression of IFN-γ and TNF-α and a strong cytotoxic phenotype with intracellular expression of perforin and granzymeB. Functionally, HLA-Cw*0702-restricted CTL show exceptionally high avidity for cognate peptide-HLA and demonstrate very early and efficient recognition of virally infected cells. These observations indicate that CD8+ T-cells restricted by HLA-C play an important role in the control of persistent CMV infection and could represent a novel opportunity for CD8+ T-cell therapy of viral infection within immunosuppressed patients. In addition, the findings provide further evidence for the importance of HLA-C-restricted T-cells in the control of chronic viral infection.
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Affiliation(s)
- Louise Hosie
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Annette Pachnio
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Jianmin Zuo
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Hayden Pearce
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Stanley Riddell
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Paul Moss
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
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Sp17 Protein Expression and Major Histocompatibility Class I and II Epitope Presentation in Diffuse Large B Cell Lymphoma Patients. Adv Hematol 2017; 2017:6527306. [PMID: 29204156 PMCID: PMC5674480 DOI: 10.1155/2017/6527306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 09/12/2017] [Indexed: 12/29/2022] Open
Abstract
Improved therapies are urgently needed for patients with diffuse large B cell lymphoma (DLBCL). Success using immune checkpoint inhibitors and chimeric antigen receptor T cell technology has fuelled demand for validated cancer epitopes. Immunogenic cancer testis antigens (CTAs), with their widespread expression in many tumours but highly restricted normal tissue distribution, represent attractive immunotherapeutic targets that may improve treatment options for DLBCL and other malignancies. Sperm protein 17 (Sp17), a CTA reported to be immunogenic in ovarian cancer and myeloma patients, is expressed in DLBCL. The aim of the present study was to investigate Sp17 epitope presentation via the presence of a cytotoxic T cell (CTL) and a CD4 T-helper (Th) response in DLBCL patients. A significant γ-interferon CTL response was detected in peripheral blood mononuclear cells of 13/31 DLBCL patients following short-term cell stimulation with two novel HLA-A⁎0201 peptides and one previously reported HLA-A⁎0101-restricted nine-mer Sp17 peptide. No significant responses were detected in the HLA-A⁎0201-negative DLBCL patients or four healthy subjects. A novel immunogenic 20-mer CD4 Th Sp17 peptide was detected in 8/17 DLBCL patients. This is the first report of a CTL and a CD4 Th response to Sp17 in DLBCL and supports Sp17 as a potential immunotherapeutic target for DLBCL.
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50
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Aitken RJ, Mortimer GL, Gillespie KM. Type 1 Diabetes High-Risk HLA Class II Determination by Polymerase Chain Reaction Sequence-Specific Primers. Methods Mol Biol 2017; 1433:13-20. [PMID: 26659794 DOI: 10.1007/7651_2015_307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The only strategy to select individuals at increased risk for type 1 diabetes for primary prevention trials is through genetic risk assessment. While genome-wide association studies have identified more than 40 loci associated with type 1 diabetes, the single most important genetic determinants lie within the human leucocyte antigen gene family on chromosome 6.In this chapter we describe a protocol for a straightforward, cheap strategy to determine HLA class II mediated risk of type 1 diabetes. This method has proved robust for genotyping whole-genome-amplified DNA as well as DNA extracted directly from human tissues.
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Affiliation(s)
- Rachel J Aitken
- Diabetes and Metabolism Unit, School of Clinical Sciences, Southmead Hospital, University of Bristol, Bristol, UK
| | - Georgina L Mortimer
- Diabetes and Metabolism Unit, School of Clinical Sciences, Southmead Hospital, University of Bristol, Bristol, UK
| | - Kathleen M Gillespie
- Diabetes and Metabolism Unit, School of Clinical Sciences, Southmead Hospital, University of Bristol, Bristol, UK.
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